we also do not have the day to day of the situation "on the ground" as we do now. Imagine a situation where the US military goes into a city of tens of thousands and puts every one of them to the gun. How fast would that get around the world?
Almost any siege throughout history occurred like the dude said earlier. If the area would resist, The army would roll in there to kill pretty much everyone and scatter the rest. If an area would surrender, give up some supplies and people for the army and maybe pay tribute... the area would usually be allow to continue existing.
let's go for hitler/nazi german because we have a lot more evidence of what he did. He rolled into places and separated "second class citizens" and groups that the mainstream people didn't much like anyway... and killed them. The nazi regime also made many people flee for their lives and the lives of the people they loved.
I don't have numbers but imagine that 1/3 of the people in a country leave/get killed. unemployment goes away instantly and all of the property of the leaving/killed party is then used for the rest of the group. The mainstream part of the group is enjoying better services from the government, more jobs, and the people they didn't care about/for are gone. That is something that suckered alot of people in about nazi germany.
now, on the flip side of destruction, think of Denmark. They knew they couldn't fight germany. So, they went along with Hitler on paper but while the cat is away the mouse will play. The Danish people/government ran many programs to get the Jews/undesirables out of danger or resistance groups in general. Heck, If you want some ballsy reaction to hitler, this is awesome http://en.wikipedia.org/wiki/Telegram_Crisis
basically, the "peace" we see in those times just looked like peace from a distance... upclose it was brutal.
Consider the IED: improvised explosive device. It allows an unhappy conquered person to leave a deadly bomb where they know an invader patrol will pass and then detonate it while being potentially miles away using a phone or other system. This means a guerrilla fighter can strike many many times regardless of terrain and potentially never be caught. To achieve the same result in ancient times would require both favorable terrain (hills to shoot from, trees to hide in) and a good escape route, and even then such a person would have a fair chance of being caught and killed.
That said, it is not as simple as saying that they could do it then and we can't do it now. Ancient conquerors weren't always as successful in suppressing conquered countries as your question implies. The Napoleonic wars are a fair example: the French invaded Spain in 1807 and occupied the entire place. Things went... poorly for them. Partisan fighters sprang up all over the place which played hell with their supply chain and forced them to allocate large numbers of people just to make sure messengers got through without being executed or captured. The word guerrilla was in fact invented for that war. This was a major contributing factor to their eventual defeat by the British and Portuguese.
http://www.neh.gov/humanities/2010/januaryfebruary/feature/the-spanish-ulcer
To be honest, this is a very complex question which I feel should be split into two. Your first concerns that of ancient conquerors and the context in which their conquests were fought in. The second one has to do with counterinsurgency in modern military history (which is my expertise!) and really can not be compared.
I think it would be better if you re-posted the first question without taking into account the modern aspect to get a more precise answer.
This is a very complex question to try to answer. I'll answer more for how Alexander or the Persians would in comparison to the Soviets in Afghanistan or the French or US in Vietnam. (Pardon any spelling or grammar mistakes, on my phone at the moment, will edit when I get home).
First, bear in mind that these early conquerors' empires were not created without asymmetrical resistance like the Mujahhadeen or Viet Kong. Take Alexander's campaign in Sogdiana (I explained this in another thread, will link soon) and Bactria; he had administrative and political control of the area, but there were Sodgdians and Bactrians resistance groups that harried them for two years, causing his campaign to come to a grinding halt until they were suppressed. This wore down the morale and number of his soldiers. Imagine if they had fought a regular war against Alexander; the Sogdians would have been destroyed post-haste, saving Alexander time, money, men, and morale. With his soldiers in better spirits, they might not have refused to march across the Indus. Alexander could've become the king of India as well.
Secondly, uprisings were a massive problem even after the area was secure. Egypt was lost from Persia from the time of Artaxerxes II until Artaxerxes III reconquered it 57 years later. Uprisings happened constantly around the empire, Babylon was an extreme hotbed of dissent against the Achaemenids.
Thirdly, conventional 20th/21st century armies could/can defeat asymmetrical resistance forces. Possibly the best example of this is the Brits fighting the Maylasian Communists from 1948-1960. How they did this was not to attempt to destroy them in battle, but to relocate the population of the country away from the rebel's heartlands.
For more reading about Alexander the Great and the Persian empire, try Alexander the Great by Philp Freeman, Persian Fire by (Book is at home). For more reading about counter-asymmetrical warfare strategems, try (TBA).