Well, sure, but other churches weren't much better at the time. The Anglican Church, for instance, never had a great track record when it came to British imperialism. The big watershed for Protestants didn't happen until the 1910 Edinburgh Conference. Not to mention that the Catholic Church's record over the past century has seriously attempted to put behind them their nineteenth century legacy, and the concordat system of church-state relations, I think, is one of the better schemes.
In my opinion it wasn't Protestant or Catholic that contributed to religious freedom, but simply the fracturing of the religious map of Europe. England and North America aren't the only example; Poland is another good case where the boundaries of Catholic, Protestant, and Orthodox produced a good century of not only religious freedom, but constitutional liberty more generally.