The role of religion in education is often debated, especially when it comes to primary and secondary education, where the minds of the students are tender enough to be influenced by vested interests. In most democratic settings, both Education and Religion are part of the fundamental rights - the right to education and the right to religious practice. I really value both these rights. The trouble however comes when the two are mixed.
In many settings religion does play a vital role in education. In a country like India, blame it partly on the lack of good public educational system, most privately run educational institutions have a religious affiliation. I do not see it as a problem. If we consider education as an essential service to humanity, then the religious institutions (not religions)that, at least in paper, claim to be dedicated to the service to humanity are more likely to end up starting schools and universities.
Unfortunately, the involvement of religious institutions in educational systems come with a premium - vested religious interests start making inroads into structure and content of the educational lives of campuses.
In my case I had by primary school education from a CSI Mission school in Ooty, Secondary education from a Catholic school also in Ooty, Bachelors degree from a Hindu college in Calicut and MBA from a Muslim run institution in Kollam. In all these places there were elements of the respective faiths pervading into everyday educational life, if not in curriculum (which was often controlled by the secular state) certainly in other ways of educational life. In my primary school it was the "Jesus is the King" prayer song followed by the "Fun - Sunday School" Everyone knows what goes in those Fun Sundays :). In my secondary school it was my deeply religious Zoology teacher who said in a hushed tone after teaching evolution theories, "Dear students, these are only meant for the exam... in reality we all know the origin of life on earth"(the "we" in this case was those students he was able to convert to his faith :). Things were not much different in my Hindu college - An arrogant Hindu Fundamental principal (fortunately he was there only during my last year) was hiring former ABVP cadres(The student wing of the RSS, so to say) as lectures - anyone's easy guess as to what impact that would have had in the campus. My Muslim MBA institute was doing it differently - they had separate prayer rooms for Muslim students. Every Friday a bus was arranged to take all my Muslim friends to the nearby Jumma mosque. Whats more, our class timings were adjusted on Fridays to accommodate the schedule of the Mosque goers.
Here is a link to an episode from the Simpsons. It is a satire on how Religion is sneaked into classrooms by vested religious interests. Check it out.