This is one of the main problems that civilized nations, and even some undeveloped countries, will face when dealing with issues of religion and politics.
Many people don't realize that religion actually is a form of government. Before there were kings and emperors and generals, there were those who said, "I can talk to God and you can't; give me your money and I'll put in a good word for you." The rules and regulations of religion are not so dissimilar from those of government (ex: Thou shalt not kill = Capital punishment debates). The structures, hierarchies, etc. all match up fairly nicely.
Separation of church and state is, in some ways, impossible. No matter how much you try to distinguish church from nation, a government is created by people, made up of people, and works for people. People have beliefs, various as they may be, and those beliefs inevitably seep into the system. Just the same, the separation is imperative in creating a truly "free" nation.
Now, as to the reasons behind the discrimination between Christian students and Muslim students, I have two points.
Firstly, the Constitution and all documentation linked to it provides every American citizen with a right to free practice of religion. That means you can worship where, who, when, and how you want (just so long as you don't have to take away anyone else's rights and freedoms to do it). Assuming that you're a Christian student, use your rights. Pray anyway, and tell any administrator who asks you to stop that all students, not just Muslim ones, have the same liberties; anyone who says otherwise is discriminating, and will be held accountable.
Secondly, you know already in some deep corner of your mind why the Muslim students seem almost "encouraged" to pray while Christians and others get the evil eye for it. We're involved in a "War on Terror" that, frankly, has gone awry. Lots of innocent Muslims are dying because of it, and the world as a whole has a changed perception of Islam now because of statements made and actions taken by the United States. This is no different than how we handle the Native Americans today. Our ancestors did something bad to their ancestors, so now a lot of federal rules don't apply to them. Same deal with the Muslim students. It's a sort of affirmative action, something to show off the fact that the Muslim students have equal rights, even if it means taking away rights from other students.
Try not to get too upset about it. Islam, Judaism, and Christianity are brothers from tens of thousands of years ago. They call God by different names, choose different manners of prayer, have different scriptures in some instances (although a lot of them line up pretty evenly), but the basic monotheism is there, along with many of the oldest stories.
Hope this answer helps.