Female circumcision usually involves cutting off critical sensory parts (ie: the clitoris) that often leave the victims unable to reach orgasm. This would be the equivalent of cutting off the entire head of a baby boy's penis. That seems like a pretty big difference to me, one that makes it rather rational to oppose female circumsion while having no issue with it on males, who have by the millions proven there's no lifelong harm from the practice.
Abbas: West Bank arson is a 'crime against humanity', vows to petition ICC (Haaretz)
from the article: Thank God for circumcision