I don't see why the act of making a question as a favourite should increase reputation. If you want to recognise a question (or one of its answers) then vote it up. And whose reputation should be increased anyway?
At the moment, marking a question as a favourite is the nearest thing we have to bookmarking/tracking a question inside of Stack Exchange itself, and hence favouriting a question doesn't mean the question should get more rep because it might not mean what you think.
What if I favourate a question because of one (or more) answers that are really good but I'm not impressed with the question itself?
What if I favourite a question because I think that it (or again, one of the answers) are an example of a really bad idea. and I want to find it again to show someone else later?
Use the voting arrows to give rep. Unambiguous, granular, clear.
Use favourites to keep track of questions. Never the twain should meet, imho.