iirc its the 30% cut they take from developers, some folks are really against it and vow to boycott. I'm sure there's plenty of other reasons but thats the first that comes to mind
If the developer looked at the trade offs between using the Mac App Store and decided to use it anyway, why should the customer care?
I would think just the opposite, I would be more inclined to use the App Store that already has my payment information on file than pay an unknown developer directly.