I don't think that's an accurate comparison because:
1. the Virgin Megastore doesn't get 30% of the revenue from the independents.
2. the Virgin Megastore doesn't get copies of the customer lists and sales records of the independents.
3. the Virgin Megastore can't slap their logo on everything in the independents' stores.
4. the Virgin Megastore cannot easily create their own competing versions of the independents merchandise.
This morning's productivity is probably blown...
Personally, I say I hate malls myself, yet once in a while I get the urge to go and buy a few things I didn't know I needed. I find comfort in the consistency of the stores, that you can go to any mall and find roughly the same vendors. Once at the mall, my choices are narrowed down (which ties into the whole Paradox of Choice http://en.wikipedia.org/wiki/The_Paradox_of_Choice:_Why_More...).
Then if you want the trust that the verification of apple gives you, you should make sure you only download software from apple.com, but the whole system is still more open and accessible by being online on websites rather than specific to a piece of software running on OSX.
I don't trust you that your website isn't spam.
I don't trust you with my credit card number.
I don't trust you that your program is well made and follows conventions.
I don't trust you that you won't install a Trojan on my machine.
I don't trust you that you won't put Adware all over.
I don't trust you that your app is bug free and won't ruin the performance on my computer.
But if Apple accepts your app into the app store, I don't have to worry about these things.
Users don't want to search through multiple websites, use paypal and drag icons into the application folder.
You will be disappointed - users will love this.