Some people say that the "Thou" refers to the then current king of England while he was visiting India. It was written originally in Bengali and was written just for the occasion.
I've also heard that the "Thou" can refer to God.
There is some controversy about having JANA GANA MANA as the national anthem because many Indian Nationalists don't want to have a national anthem that is based on a poem written for the King of England. They say that it is like being subjugated to the British all over again.
I don't know about all of that, but I like it because it's pretty.