Quarries themselves are pretty well balanced. As others have said, it's features added by other mods that really make them overpowered, if anything does. With just BuildCraft, you need a lot of infrastructure to get a quarry going, especially to obtain the oil you need to power one.
Mining can be fun in the early game, especially with TC's newer tools, but it soon becomes boring. Automating it, and allowing the player to concentrate on just building more interesting fun stuff makes the game a lot less boring. there are of course, more complicated ways of automating it, using frame replacement mods like Redstone in Motion, or just frames if you're still on 1.4.7, but to be honest, I don't want to build one of those every playthrough; I'd rather come up with new stuff, and thr quarry is a reliable way to get the resources required to do just that.
In the real world, you don't just go out an mine when you need resources. You buy what you need from a company that specializes in producing said resources. You spend your existing resources to get the ones you need. A quarry isn't much different from this. You spend your resources (energy) to have minerals extracted that you need to do other things (in the real world, things that you have a comparative advantage in, in Minecraft, more likely things that are more fun). Almost all automation in minecraft can be thought of this way. I think what's most important is that the amount of resources you have to put into automating something is appropriate for what you get out of it.