I find that it’s because we are in the Western World, many people view Muslims as a threat to national security or just see them as a bad group of people. I think people in the US are quick to say that our religion or our way is “better” than non-Western people, and Muslims seem to be the current and most-widespread iteration of that superiority. Most if not all of these stereotypes and generalities of Muslims and Islam are based on fear or willful ignorance, and even racism, rather than an actual knowledgeable critique. Muslims function as today’s newest scapegoats for all things, and that is unfair. Atheists such as myself may criticize religion in general, but I can sense when members of one religion are being critiqued and members of another are being unfairly persecuted.
Christians however, are a privileged group that have used their power to do a lot of harm, and often create political and social platforms that only serve the interests of other Christians. In fact, Christians seem to be the group that most ardently opposes anything or anyone Muslim, trying to prevent the construction of mosques or trying to combine Church and State, so long as it is a Christian Church. Christians, no matter what they say, are not a persecuted group. Not to say that all Christians want non-Christians to suffer, but the ones in power are consistently pushing a Christian-centered platform, which inevitably erases others.
It’s really not necessarily a Christian-Muslim thing, but more about who is using their power to hurt others and who is suffering from it.