If they actually did target them, how did the RAF protect them successfully? (i.e., since they're still standing today)
Well, those buildings were hit. Though you're correct that they were not specifically targeted. There's a reason for that, bomb aiming simply wasn't that accurate. Which is why Bomber Command's usual target was "City Centers". Remember also, the German attacks on London, like Bomber Command's attacks, took place in the dark. Makes targeting anything small a little bit more difficult.
They did. However, WWII bombers had a CEP amounting to "one city, more or less". In extreme cases they would hit the wrong country; Dublin, in neutral Ireland, was bombed several times. Hitting a specific building wasn't going to happen except by good luck.
I know that Allied bombers were instructed to spare cultural monuments in German cities. I think it was the same the other way around... Especially because Hitler did regard the British as the Germans natural allies because of race. The war in the West was generally much more civil than on the Eastern Front.