Just finished reading up for another class, so I'll take a bit to answer this question!

In Max Boot's article in the New York Times, called "Sparing Civilians, Buildings, and Even the Enemy", he talks (mostly) about the wars in the Middle East. However, he does include a short blurb comparing/contrasting the bombing strategies to those used in WWII. A good thing that sums it up is this:

The inaccuracy of such [bombing] campaigns led World War II generals to make what they saw as a virtue out of necessity: They would engage in 'area' bombing, like the 1945 raids on Tokyo or Dresden, ostensibly intended to cripple enemy industry but really aimed at breaking enemy morale. This was accepted with hardly a peep of protest from both the British and the American public.

Personally, I think this is a pretty good description. Many of the bombing raids were very, very inaccurate, and it was impossible to know where the bombs would land.

This post has already been made on the subject, and talks about how inaccurate many of the bombing raids were. I don't think there's any real considerations for things like cultural sites, at least not that I know of. If they were considered, they were considered very rarely as far as I can tell, like in Kyoto.

Insofar as the, again, civilian casualties, I have a few things to say on the subject.

In Michael Walzers Just and Unjust Wars, he refers to the bombing of occupied France and the Vemork Raid as a sort of case study in noncombatant immunity and military necessity being at play. The Free French air force, during WWII, carried out bombing raids on occupied France, with the knowledge that they would likely kill Frenchmen working for the German war effort (who were coerced).

The pilots resolved this dilemma "...not by giving up the raids or asking someone else to carry them out, but by accepting greater risks for themselves. 'It was...this persistent question of Bombing France itself which led us to specialize more and more in precision bombing - that is, flying at a very low altitude. It was more risky, but it also permitted greater precision...'"

In this regard, we know that the French were fairly careful, even when attacking things that contributed to German war capacity, when bombing French civilians. But the risk-taking was difficult to undertake. Walzer also brings up the example of Vemork, where a heavy water plant was destroyed by Norwegian commandos operating on behalf of the British Special Operations Executive. The first attempt failed, but the second worked. Later in the war, after production had been resumed, security was considerably tightened, so the plant was bombed from the air by American planes. The bombing was successful, but it resulted in the deaths of 22 Norwegian civilians. Military generals justified this with the principle of military necessity; they felt that this would stop the Germans from getting an atomic bomb, and the casualties were unavoidable, so they had to do it.

Now with regards to enemy civilians, there's even more information that suggests this was the way the Allies approached their bombing runs. Walzer goes into the idea of noncombatant immunity and how to evaluate it, but I'm not going to go into that because it's his belief, not necessarily the ones the Allies used.

Walzer does, however, point to something called the idea of "Supreme Emergency". This idea, that we must kill civilians in order to win the war, was one that was taken by the Allies in WWII (he argues). Ignoring the obvious examples of Hiroshima and Nagasaki, let's look at the Allied bombing of Germany from February 1942 to the end of the war. Arthur Harris, who directed that strategic bombing, was what Walzer calls "...the determined advocate of terrorism, resisting every attempt to use his planes for other purposes." Harris, for his part, was never treated with high regard after the war, because of his part in the bombing. No matter how much it was claimed to have helped the Allied cause break the will of the Germans, Bomber Command was "slighted and snubbed", as Harris was not rewarded with a peerage. There is a plaque honoring the pilots of Fighter Command who died during the war, listing them all by name. There is no such plaque for the bomber pilots, though they suffered far heavier casualties.

So we know the bombers weren't honored after the war, despite the justifications given. We know that people were killed by terror bombing, or at least bombings designed in equal part to destroy industrial capacity and demoralize the populace. I think many of these points today are not disputed very widely, though if someone can correct me I'd be glad to hear it.

How helpful the bombings actually were, is another story entirely that I'll leave for someone else to cover, if they so choose. But this fact should give you an idea of how the Allies viewed the bombings of civilians as regrettable but unavoidable; the Tokyo bombings, over the course of two days, killed roughly 100,000 people and destroyed 267,000 buildings, dropping 2,000 tons of incendiaries and 330 B-29's in the process, according to this article. I can source it to something more scholarly if you'd like; regardless of the exact numbers, it's very clear that the goal was not to destroy military installations alone.

Consider again the example of Dresden. Biddle estimates that 25,000 civilians were killed, at least, during the Dresden bombings. As Biddle puts it:

...the attack on Dresden was similar to other air attacks the Americans and the British carried out in January and February 1945. Dresden contained military targets, and it met the fate that had befallen other German cities, such as Cologne in 1942 and Darmstadt in 1944 - and that would befall still more, including Pforzheim and Wuerzberg, before the war ended. In terms of lives lost and damage done, the Dresden raid was less destructive than the now largely forgotten American attack on Tokyo [which I talked about above! - tayara] on the night of March 9-10, 1945, which killed 100,000 Japanese. And it did less damage than the devastating firestorm Britain's Bomber Command visited on Hamburg in late July 1943. But what does set Dresden apart is rarely explored in analyses of the motives for the raid and the events surrounding it: that an erosion of moral sensibilities had cleared the way for attacks on a city the Americans and the British knew was swollen with refugees.

Biddle's account is very clear, I think, and speaks for itself. Another, from later in his article:

In September 1939, Roosevelt had issued an appeal for every government engaged in war to affirm publicly that it would not be the first to bomb civilians or 'unfortified cities'. In response, the French and British jointly declared that they would spare civilian populations and government property. The Germans said they welcomed the president's appeal and would bomb only military targets, but their attacks on Warsaw and Rotterdam quickly rendered these claims hollow. By 1945, the last tatters of the pledges of 1939 to protect noncombatants were removed.

Again, speaks for itself. And finally, one last point from Biddle's excellent article:

The willingness to overturn previous constraints also revealed the urgency and anxiety that colored British and American deliberations at that moment in the war. On December 30, 1944, Generaly Henry "Hap" Arnold, the Washington-based commander in chief of the US Army Air Forces, told Spaatz that he was concerned about the Germans' reviving their fighter plane production. 'I want to impress upon all of your people that we will accept with satisfaction any increase in tonnage, no matter how small, provided you will drop it where it will hurt," Arnold wrote. At the same time, Robert Lovett, the US assistant secretary of war for air, drew up a detailed memorandum arguing for an expanded air effort - in particular, for spreading the attacks to Germany's smaller cities and towns...Though the Americans strongly preferred to strike specific industrial sites when weather permitted, the bulk of their raids through butts were, in essence, area raids. But to distinguish their efforts from those of the British, the Americans continued to define these attacks in the language of precision bombing. But their frustration as the war dragged on eventually made the Americans more amenable to waging air attacks that were designed, at least in part, for their psychological effect on the enemy. On February 3, 1945, they launched a massive attack on the center of Berlin to aid the Soviet advance and hasten Germany's surrender.

I think these articles and points speak for themselves. Perhaps at the start of the war, the idea and goal of bombing was to avoid civilian casualties...but the war quickly shifted to a total war that was less concerned with the bombing of civilian casualties, because it had such urgency that such care could hardly be afforded by most bombing raids. And as the war dragged on, and stiff resistance even in the face of defeat came from the Japanese and the Germans, civilian and terror bombing became more and more common and justified by Allied leaders. Again, I leave the question of effectiveness to others, but I don't think it's disputable that German civilians...were never really the top of anyone's list when fighting people like the Nazis, even if they possibly should've been.

Sources:

Walzer, Michael. Just and Unjust Wars: A Moral Argument with Historical Illustrations. New York: Basic, 1977. Print.

Boot, Max. "The Nation; Sparing Civilians, Buildings and Even the Enemy." The New York Times. The New York Times, 29 Mar. 2003.

Tami Davis Biddle. Sifting Dresden's Ashes The Wilson Quarterly (1976-), Vol. 29, No. 2 (Spring, 2005), pp. 60-80

Kyoto was spared from large scale area bombing (or indeed atomic bombing) during WWII because of its significance as a cultural and religious centre. Henry Stimson, the US Secretary of War, felt that bombing Kyoto would further alienate the Japanese population and drive Japan into Russia's arms after the war. As such, Kyoto was not to be bombed without his permission and in the end was spared the wholesale destruction that other large Japanese cities had undergone. You can read excerpts from Stimson's diaries here, which also provide some information about why area bombing was felt necessary to destroy Japan's war output. Kyoto's cultural and historical significance is also mentioned by Stimson in his "The Decision to Use the Bomb" (February 1947).

Interestingly, Stimson had visited Kyoto as a young man and loved the city so much that he returned there on his honeymoon long before the war. Some have suggested that his decision to spare Kyoto was based on his emotional connection to the city, and that he concocted the "official" reason for its salvation after the fact.

In either case, Kyoto was spared widespread destruction because of its cultural significance, certainly to the Japanese people but perhaps also to Stimson himself.

Edit: additional source.

I hope someone can elaborate on this, but didn't the allies bomb an important Christian religious site in Italy? I recall that they asked for volunteers who would be willing to do it. Does anyone know what I am talking about?

Sorry if that's off-topic.