They can, though some people and science will tell you they can’t, due to the leaching of plastic chemicals into your food (yuck). But I do, and I’m not dead. Then again, I’m a starving grad student. I’d eat pretty much anything that was dead.
There’s a lot of debate about whether it’s safe to heat food in plastic, but I just read this Good Housekeeping article where they tested something like 30 different kinds of plastic containers and found that none of them leached any significant amount of chemicals into the food when heated. The article is pretty convincing, so I’d say, microwave away! =)