Why are you forced to sync purchases with iTunes?

So I finally had time to upgrade both my iPad 2 and iPhone 3GS to the latest software. I decied I would do a restore just to get rid of all the mess. At the same time I decided that now with the cloud (and anyway in my case) it wasn't very helpfull to have all my apps synced with iTunes on the MacBook I have. So I did not check that under the settings of my phone.

Basically the only thing I sync from my MacBook to my iPhone is music. Nothing else. And I don't sync anything at all between my MacBook and iPad 2. All calendars, mails, contact etc are synced through WIFI and iCloud/gmail.

Now after this I downloaded the apps I use on my iPhone and connected my iPhone to iTunes just to back it up (I don't back up in iCloud). And for some reason iTunes tells me that it needs to transfer the purchases from my iPhone or they will be deleted from my iPhone (eventhough I have disabled app syncing with iTunes). My simple question is WHY!?! I don't have a need for this and don't want this. Why can't I just disable this?

So I went on and took the risk by clicking "do not transfer". And iTunes just goes on transferring them anyway. What is this about? I don't want all those apps on my MacBook. My iPad, iPhone and MacBook are all three different deviced with a different selection of apps. I just want to have the apps on a device that I need and don't need any other useless apps on there. So I don't want any iPhone/iPad apps transferred onto my MacBook.

So can anybody help me out here? How do I get this the way I want it? Am I overseeing something?