A lot of stuff was rooted in banning the abuses by the king of England and ending European problems. There were wars in Europe between protestants and Catholics. There was also the issue of kings/queens trying to force their religion on everyone. The new king is Catholic, now we've all got to stop being protestant and be Catholic. Freedom of religion put an end to those problems. They did not consider the problem of Islam and Judaism. Muslims were a non-factor, and they didn't think there would be a large portion of them let in here.