The man hours to perform a proper strip and prep consume a lot of the cost. Taping off all the skin joints then manually stripping those areas is tedious time consuming work...but the proper way of doing things. Of course, then you have the reassembly and balancing of control surfaces. Slopping on a bunch of stripper then pressure washing it off can save a lot of labor cost but, will you have an airworthy plane once corrosion takes it's toll in those lap joints/faying surfaces? There is no paucity of reports of airframes being written off from such poor practices.
All true, plus the cost of materials and the cost of complying with environmental regulations are quite high. I spent a while talking with my paint guy when my Beech was done last year. The overhead of maintaining a facility large enough to paint biz jets ain't cheap, either. They have to have sealed lights, switches, etc., special air handling, fire suppression, and so on.
Unlike a car paint shop, they're not turning a job out every day or two, either. My plane was in the paint shop for over two months. I think he had about a half dozen planes in the shop, in one stage or another. I'd guess on average that they're completing about one job every two weeks, though I'm sure it varies a lot with airplane size and the complexity of the paint.
Plus they have to cover the cost of eating inevtible mistakes. When I first saw the airbrushed tail art on my plane, it was excellent but the height wasn't the same on each side, so they had to remove it from one side, redo the base paint, and then bring their airbrush guy back in for another day. The shop was great about doing it, no hassles at all, but I know it ate into their expected earnings.
A reputable shop will also flag any problems, like corrosion or skin damage, that they may find during disassembly. Some shops will cover small repairs up to some dollar limit, but will contact you if they find something bigger for instructions.