The specific circumstances of the case would need to be considered in terms of what you were protesting. Was it academic in nature? Did it have something to do with say not providing your required rights under the Americans with disabilities act or some other legal protection? It does depend on what you were protesting in terms of what your rights would be in the process. If you find yourself being charged by the school, it's not an unusual situation.
Unfortunately, if the school has misgivings about what a student was doing or the students say thoughts are being outspoken about a matter, it can lead to potential charges. Whether the school is within its rights to do so, is an entirely separate consideration. Understand your rights and how to protect your rights and interest through the process is incredibly important.
An experienced attorney advisor can help you best analyze the situation at hand and can help you best understand and navigate the process moving forward so that you can defend yourself, especially against allegations that are unwarranted.