My father has been a beekeeper for about 12 years now (he was when I was really little too, before this bee crisis) and so I've worked with him a bit on his hives and helped him with a lot of research. By the way, I'm on my phone here, so if you want a reference later, say something and I'll throw them in later.
There seem to be a number of factors that can lead to colony collapse, some direct practice, and some environmental. My dad lost a lot of hives the first few years since he started up again, but good practices have helped him retain nearly all of his hives for many years now.
One big thing, obviously is our ubiquitous use of pesticides. While their producers claim the chemiclas don't affect bees, bees kept pesticide-free don't die as often.
Another is global climate change. Bees hibernate in the winter. They pop back out in the spring. A long warm patch toward the end of winter followed by another significant cold-spell, is murder on a hive. They think it's spring, so they set to work, and then freeze to death. Equally dangerous are winters that last too long. Bees gotta poop like anything else, but they can hold it during hibernation. If the winter goes too long, they can't hold it any longer. They poop in their hives and poison themselves.
Another factor is one that most big commercial beekeepers will deny. Queening practices. A queen can run a hive for many years. The middle years seem to be the most stable and productive. However, that's not too good for expanding your business. A stable hive won't branch off with a new young queen more than once every several years. So keepers go in and kill the queen every two years. This causes the hive to panic and produce a bunch of queens at once. Often, two or three queens will split up the hive, so next year you have 2-3 hives instead of one. Brilliant, right? Unfornately, these new hives are totally dominated by younger bees who are, of course, less experienced. The hives never get a chance to really stabilize.
But denial of this issue means that hive collapse is then chalked down to "it's a fucking mystery! The bees are just dying for no reason". Once I convinced my father to completely ignore convention and let the queens be, his hive collapse issues reduced significantly.
Then there is Africanization ("killer bees"). An Africanized hive is more aggressive and less productive than a traditional one. Most beekeepers no longer consider such hives as "honey bees", and destroy them ASAP (before they spread). But the thing is, the change is more behavioral than genetic. Africanized bees take over a colony, kill most, and convert the rest. I've come to think of it as a bee revolution.
You can still work with these bees, but you have to be more respectful. For example, with traditional, peaceful honey bees, experienced hands don't need to bother smoking them to sleep or even going full out with the suit (as long as you're not dumb enough to wear dark clothes). You just pop open the top, pull out a shelf (not the queen's!) do what you have to do, and pop it back in. The bees get a little annoyed, but you're not gonna get stung. Try that with Africanized bees, and they'll kill you. You have to smoke them. You have the be careful and cautious. You have to use proper gear. Most inconveniently, there are much stricter rules governing their seasonal transport.
I don't know if peaceful, essential honey bees will survive this era, but I don't believe their disappearance will be a mystery. Some beekeepers have learned to respect their bees, but the bigger commercial ones seem content to throw their hands up and lay all the blame on pesticides and weather.
