You are have the right to believe what you choose.  You said "our" flag, this means either it is also "their" flag as American citizens and they have the right to protest if they choose, or it is "your" flag and thereby you are dictating the rights of others.   
The wide-spread NFL protest only occurred after PDT made this political in nature.  If the owner of the private property agrees to a protest, the protest can be justified.  Free speech in public should be allowed regardless of content, although public safety is paramount.  Universities are usually quasi-government organizations and need to balance the consequences of politically motivated speech.