John Milton grew up within a Puritan family. His education was grounded within religious ideology. He attended St. Paul's Cathedral School at the age of 12. Milton then entered into Christ's College (attending from 1625 through 1632).
Towards the end of his writing, Milton began to question the Protestant religion and ideologies (Milton did not seem to have issues with all Christian religions).
It seemed that Milton examined individual Christian religions and played with their differing ideals. Instead of being against a religion as a whole, he would be against specific aspects of the religion. In essence, Milton was a little bit of Presbyterian, Protestant, Quaker and Puritan. Unable to follow one religion's ideologies in whole, Milton simply followed the ideologies from each which he tended to agree with.