Where does Android keep app permissions? I have a rooted Android, and I want to disable (not read/write/execute) permissions to an app (for example, I don't want it accessing the camera or the phone).

Where does Android keep those permissions? Is it in a database somewhere?
App permissions are defined in the code of the application (the manifest to be exact) and cannot be changed without actually "un-building", changing and then rebuilding the apk again.
the solution you're looking for is using permissions controlling/restricting applications.

Here are some examples for these kind of apps:

LBE Privacy Guard

PDroid

App Ops - Permission Manager