Isn't it because it just ends up making the department have even more work? It probably doesn't apply to all cases, but when Wikipedia had their donation (I think they had a '50% goes to charity' thing) it had a $5 minimum and you could also choose which non-profit organization you wanted the money to go it, but they asked you that you not do this, since it just makes them have even more paperwork.
http://wikimediafoundation.org/wiki/Donate/Questions/en#Why_is_there_a_minimum_donation.3F
--
http://i.imgur.com/wl4c3.jpg