Why do your muscles hurt after exercise?

I always wanted to know why my muscles hurt so badly after exercise. Today PZ Myers explained it in a very long article on his blog Pharyngula: Why do muscles hurt after exercise?. It is a really long text and the target are his biology students, so I didn't understand very many of the details expecially at the beginning of the article where he states "But you knew that already." :D

But when you get through the long thing you get a summary in mostly plain english which I would like to quote here:

So why do your muscles hurt after exercise? There are three major reasons.

1. a transient accumulation of metabolic byproducts that can cause some soreness during exercise.
2. Changes in ion concentrations in the muscle that can cause some fluid swelling, and also triggers active remodeling of the proteins for growth.
3. you broke 'em. You can cause micro-tears and internal disruption of muscle proteins that can actually force your muscles to throw out and reconstruct whole fibers.

What should you do if your muscles are aching after exercise? [...] reduce the intensity of exercise to light, submaximal exertion and stretching exercises, which have been found to reduce soreness and promote more rapid recovery of muscle tension. Light massage is also good for reducing pain, but hasn't been found to do much to facilitate actual physical recovery otherwise.

But I encourage you to read the whole article and don't be unnerved by the first 1/4th of it, after that he delivers some interesting facts we normal people actually can understand.