Disc's aren't bad. Their modulation and smoothness are great. I was astounded by their smooth, sure stopping power. I just don't prefer them.

They weigh more.
They're down there around the axel and can get in the way. You have to work around them.
It's something else I'd have to learn how to fix. I know canti's, vee's and calipers.
More parts.
I'm given to understand that they apply different forces/stresses on the wheel—spokes in particular. Someone else who understands that aspect better can fill you in. Cyccommute, I believe, gave a rational explanation.

Anyway, those reasons won't hold water for a lot of folks and that's all right. As I said—it's personal preference. As most things are. I don't think they're bad at all, I just don't prefer them. It's mostly about the weight and added complexity for me.