Part of the problem, I imagine, is that software companies want to maintain a degree of control over how their software is distributed.
Take your windows example: $250 retail, $260 online. Let’s pretend the reverse were true ($260 retail, $250 online)-
That means that (vista sales performance aside) in theory, I could make an out-of-my-garage business downloading copies of vista for $250 a pop, burning them to DVD, and selling them for $255. By making online copies cheaper, Microsoft has just CREATED a retailer who they have no business relationship with, who has no return policy or customer service department- Brick Mortar’s have more purpose than moving software; they serve as a buffer between the customer and the creator, handling things like refunds basic customer service. Also, if instead of going to CompUSA for versions of windows, millions of users were buying from thousands of home-retailers like my hypothetical self, it would be nearly impossible to apply pressure and stop us from, say, writing the word “STUPID” on every copy before we sell it, or displaying it in the same “aisle” as a copy of Ubuntu, or whatever- A chain like CompUSA, they could just stop providing the supplies to. The garage retailer, they’d have to increase the price AFTER RELEASE of online downloads in such a way to cripple our business- which would be a PR nightmare.
So, I think it’s probably more than just charging lazy-tax. They’re just trying to put a leash on distribution of their own product