It very well may not be fair. Is the school allowed to pursue misconduct charges against you? They may or may not be allowed to do as such. It depends on the particular circumstances at hand. It depends on the nature of the comment, what was specifically stated. If it was of a sexual or racial nature, that would be a concern. If it was a threatening comment that would, of course, be a concern.
That being said, students do have the freedom of speech. It is a limited right. A student and others at a college or university would have the right to express themselves in an appropriate manner, with the school considers to be appropriate versus what is, in fact, appropriate there could be a disconnect at times. Being accused of making a comment that could lead to or would lead to disciplinary charges is definitely a potential scenario. It is a serious situation. You have to understand what your rights are in the process and how to best protect your rights. An experienced attorney advisor can help you do so. They can also help you best understand and navigate the process and should be involved as early as possible.