Unfortunately that is where it falls apart.
The fund-raising model that "works" for Wikipedia is very different from the Flattr model. And I am not convinced that the Flattr model can scale up to the Wikipedia level.
(not to mention the fact that donations would be a lot more random, difficult to track and will come in fits & spurts; which is basically useless when you reach the levels of money the WMF is after)
If wikipedia adopts Flattr as their micropayment solution, overnight tons of people will open a Flattr account.
I do not think this would happen as easily as suggested.