It is actually not much at all - Cafepress makes items ONE at a time, and its basically store price for good quality shirts (we are talking quality cotton etc)
It depends the shirt/hoodie, but basically its only like $4 or something... Not much at all. Some things don't even have marked up price ($0 for FP) and are just there to promote FP to people you meet.
If we ever have enough $$$ to invest in shirts, we will pre-pay for "screen printed" ones (different process, cheaper but you need to order A LOT) and we will be able to: sell them cheaper, AND provide more money per shirt for FP.