Good Question. Two known reasons. 1. The song is primarily in Sanskrit, which is a Hindu language, and 2. The song aims at making the chanter accept bowing at Mother Country, which is a Hindu concept. But why is it important so sing Vande Matarm? Even among those who have no objections in singing Vande Mataram, there are many tritors. Patriotism is out of fashion, buddy. Look at the shortage of Officers and Jawans in the army.
