Okay, so a lot of times it's just being stuck waiting for a mile-long cargo train to pass, but sometimes it's more interesting than that!
Expect Delays: Why Trains Slow Down When It's Hot
Tl;dr: train tracks used to have expansion joints and could deal better with extreme temperatures, but the railroad industry found that meant they were harder to maintain and resulted in slower, more uncomfortable rides. Railroad companies got rid of expansion joints in favor of longer sections of track, and while for the most part this had made train travel more efficient and more profitable, it means that the metal rails (prone to expanding when they're hot) do some wacky stuff now that they have no wiggle room:
Trains need to slow down to traverse this bends safely (and presumably to keep from making them worse, since more speed = more friction = more heat).
This is relevant to me because I am planning a big cross-country Amtrak ramble in June of 2015, with a large bulk of it through the Southwest. I had always assumed Amtrak delays were because of other trains using the rails (since Amtrak does not own many of the rails it uses, only the trains). I never realized there were other issues inherent with the mode of transportation itself.
This isn't making me rethink my trip, however. I've made generous allowances for delays in my plans, and I look forward to traveling the country in way I haven't really experienced before!