In a pluralistic society, it is critical that we respect the religious beliefs of others and allow others to practice their religion as they see fit. But being able to practice one's own religion does not allow you to force your religion on others (I've written about this re: the contraception mandate), even on your children. And your right to religious freedom does not allow you to inflict bodily injury or cause physical harm to another.
In the West, circumcision is primarily performed on infants, who are unable to consent to the procedure. It is generally performed for non-medical reasons, primarily because of religious beliefs or (especially in the United States) for cosmetic purposes. The procedure is incredibly painful, permanent, affects the child for the rest of his life, can dull sexual sensation, and can lead to bleeding and infection. Recently, for example, in NYC, 11 babies contracted herpes through a (rare) circumcision ritual; 2 of them developed brain damage and 2 died.
As a feminist, I believe in bodily autonomy. I think no parent should have the right to cut off a part of their son's penis without their son's permission. If a boy is of an age where he can consent and decides to get circumcised, then that should be allowed. But infant circumcision allows for a non-medically necessary, permanent surgery to be performed on a child without his consent. Moreover, as much as banning male circumcision can be said to be politically motivated, racist, or to violate a group's religious freedom, allowing for a religious exemption belies another form of racism, cultural imperialism, and the West's own religious hierarchy. US federal law, for example, currently “makes criminal any non-medical procedure performed on the genitals [of a girl].” There is no religious exemption, and few people protest that this violates religious freedom. Few protest the banning of female circumcision in Western countries or in Africa and the Middle East and it is popularly condemned as barbaric and misogynistic. Moreover, when the American Academy of Pediatrics suggested that doctors could perform a ceremonial pinprick or "nick" a girl's genitals to prevent them from receiving a full circumcision overseas, the move was met with outrage from the feminist community. So why is it ok to do more than "nick" a boy's genitals - even for religious or cultural reasons? Cologne's ban on infant circumcision doesn't violate the parent's rights; it preserves the boy's.