Religious freedom does not mean anyone can do anything and call it religious expression. Do you really think praying and building a mosque are the same thing?
No of course not. Praying is guaranteed right in the First Amendment, but building the mosque is decision left up to the city council who obviously have an ideological bend to the left. The voters of NYC didn't vote for the mosque, the city council did.
Had I been a member of the city council, I would have said "no" to the mosque because there's 20 other mosques in Manhattan, and about 20 or 30 in each of the other four boroughs of New York City. Imam Rauf runs a mosque about 12 city blocks from the site of this proposed mosque.
I'm free to pray wherever and whenever I want. Praying is religious expression.