Credit card fee structures make it a little complicated. Generally speaking, you'd want to pool both the input and the output, and then use paypal or something similar -- i.e., require a minimum of a couple dollars to be put in escrow, and then actually flush the payment once it reaches a couple dollars. That way, transaction fees don't totally overwhelm actual payments.

I haven't seen general-purpose systems optimized for micropayments in this way. Aside from flattr, I've seen token-coin (a blogging platform, essentially), and places like patreon roll their own system internally.