Go ask the Mormons, who suffered incredible persecution. Or read the history of Catholics in the United States, who had an entire political party founded in opposition to their presence. Quakers' pacifism has often been viewed with suspicion and hostility. And that's just in the Christian family of religions--- we could spend days cataloging the prejudices and insults offered to Jews, Wiccans, Native American beliefs, or outside-the-mainstream small groups. Add to that the scorn you might receive for not having a religion at all. There has never been a time when religious differences were accepted, and those differences have often been met with violence.
So it's sad but not too surprising that there's political hay to be made in Muslim-baiting. That mosques are attacked by arsonists or accused of being centers for terrorist indoctrination. That somehow the placement of worship places is a public, rather than a private, concern.
Tolerance shouldn't be a hard lesson, though, even for the most fundamentalist of Christians. You don't have to adopt an agnostic attitude, or admit that all paths to God contain some truth, or consider the possibility that your beliefs might strike others as strange. You just have to adhere to what Jesus instructs in very clear terms:
"You have heard that it was said, 'Love your neighbor and hate your enemy.' But I tell you: Love your enemies and pray for those who persecute you, that you may be sons of your Father in heaven. He causes his sun to rise on the evil and the good, and sends rain on the righteous and the unrighteous. If you love those who love you, what reward will you get? Are not even the tax collectors doing that? And if you greet only your brothers, what are you doing more than others? Do not even pagans do that? Be perfect, therefore, as your heavenly Father is perfect."
Or as Paul approvingly quotes from Proverbs:
"If your enemy is hungry, give him food to eat; if he is thirsty, give him water to drink. In doing this, you will heap burning coals on his head, and the LORD will reward you."