Look at it this way, say I play the City of Heroes game on my digital device. I use my digital device to access the application to play the game but I don't pay my monthly fee to Apple or Microsoft or Dell or HP or IBM, I pay it to the company that makes City of Heroes. I just use an Apple (etc.) product to access the game because Apple (etc.) is just supplying the hardware for me to access the game.
Marvel and DC will do the same thing. They don't need to pay Apple (etc.) to supply you comics to read on your pad/tablet. They can do it through their website and completely cut out the middleman. They will get the whole 99 cents (Well, at least most of it. Running the website will cost something but it will be a pittance compared to what they pay to distribute paper right now.)
While Apple is controlling of what programs are run on their devices, applications already exist that display .cbr and .cbz files on the iPad and it's free. Marvel doesn't have to pay anyone to sell their comics digitally. They can and will do it themselves.