The biggest problem with most shops is attempting to tackle a spectrum of automobiles that is too large as opposed to single model/brand specialization. This can also blanket into going outside of your specialization in a certain area of said automobile as well.

Example: You advertise that you're a transmission shop and you do window tint just because the customer asks for it. It's an extreme example but I think everyone can understand it. It's really silly to try to be everything to everyone who walks through the door. Be good at what you do and corner a niche market.

Being a former employee of several shops, I can tell you that it's annoying and frustrating when you work on high-performance brand specific vehicles and the owner thinks that doing a water pump on a Duratec Taurus is perfectly okay. You've gotta stop, research, call around and stumble through it instead of just making money on what you know.