For one simple reason that constitutionally it is our naional song. BUt there are several others.
We all love and respect our mothers (I am sure every religion permits that) and in this song swear to have the same spirit for our motherland who provides us all that we need. Why should there be a problem?
It was written by Bankim (in Anand math) where it was sung by the local people while fighting the British. Hindus, Muslims, Sikhs and others fought in the same spirit for freedom. Why should there be a problem about singing it? Music is not prohibted in any religion. Our greatest musicians have been Muslims (Ustads Akbar Ali Khan, Bismillah Khan, Naushad, Khayyam,Talat, Rafi, Amzad ...) as well as those from other religions.
But let me admit that I am not aware why Quaran- e- shareef would prohibit that? I did buy a translation of this book sacred to billions but am yet to read it.
But, probably, instead of forcing this beautiful thing down the misunderstanding and suspecting people's throats, a better way may be to explain the meaning, spirit and significance of the song to any Indian patriot. Let dissenters also explain.