The Ultimate Question

Why do good girls like bad boys?

The assumed definition of "bad boy"*: a male who only uses females for sex.
The actual definition of "bad boy"*: a male who has ever let down a female at any point in their life.
*Same goes for "bad girls" towards males. As well as females towards females, males towards males, etc.

I have a lot of friends who consider themselves "good guys" and wonder why the girls they like go for the "jerks" or "bad boys".
First of all, you're assuming there are no "bad girls". There are plenty of girls out there who do the same things to guys as the "bad boys" do to girls. Also, considering the girl chose a "bad boy", how do you know she's not in fact a "bad girl", as well? Yes, she may be a nice person, but that doesn't mean she doesn't have a bad side to her.
Second, you're generalizing boys into two categories: good and bad. We all know for a fact that there are many guys who have treated some girls badly, but treated others like angels. It all depends on whether they really like them or not.
Finally, to all you "good guys" out there. Are you really a good guy? Have you ever let a girl down? Well, if you have then you've probably been considered a "bad boy" at one time in your life, because the person who lets the other person down is considered the "bad" person.

In conclusion, it's all about personal preference. If the "good guy" doesn't get the girl, that probably just means she is not the right girl for him anyway. If she prefers to be treated badly by someone, that's her choice. One day, everyone will find someone who loves them for who they are, live happily ever after, blah blah blah. The end.

Q&A
If you let someone down, are you actually a bad person? 
No. It's better to let someone down when you know you're not attracted to them rather than lead them on and have it end even worse later on.
If she didn't choose the "good guy", does that make her a "bad girl" or even a bad person?
No. She is probably just more attracted to the "bad boy". If she changes her mind and gets tired of the "bad boy", she'll eventually look for someone else.