Most schools in India are secular. They not affiliated to any religion in particular. Some schools, on the other hand, are started by religious organizations.
It is perfectly all right for schools that are run by religious organizations to promote or teach their religion.
It is important however, for secular schools to be truly secular. The 'G' word must never be mentioned. Now, before you go about shouting me down as an atheist, let me clarify that I believe in religion and am a temple-goer. I however believe that teachers should never mention religion or anything related to it.
Every religion is different. Yes, we've heard many times that the fundamentals of every religion are the same. However, there are some basic differences between the major religions.
Christianity and Islam say that there is one omnipotent God. Hinduism has a pantheon of Gods, all omnipotent. Jainism is an atheistic religion and says there is no omnipotent God and places 'karma' as the ultimate force.
This is a very major difference between these religions.
Most schools however (unintentionally?) propagate the monotheistic line of one omnipotent God who helps us or punishes us. This belief sometimes becomes so ingrained into children that they find it very difficult to reconcile or accept any differing belief even if it is the one their family follows.
Religion is an intensely personal thing and it is entirely up to an individual whether to follow it or not and if yes, which one to follow. It is definitely not something that should be learnt at school.