The biggest reason is, a large portion of users have really bad taste.
Of course, you could argue that taste is subjective, but it isn't. There is good taste, and there is bad taste, just like there is good design, and bad design.
For proof, look at the home screens of the majority of jailbreak users, they are hideous, absolute eye soars, installed by somebody with really bad taste.
The thing is, ugly UI's don't sell phones, beautiful UI's sell phones.
If I'd never seen an iPhone before, and a geeky kid showed me his iPhone, with a custom ROM, neon, glow in the dark Winterboard theme installed, I wouldn't buy one. I'd think it was ugly.
This is what Apple doesn't want.
Apple allows some customisation, but never enough to make your iPhone ugly.
Beautiful Handcuffs shall we say.