But, in the end Charles was the foe of any religious freedom and an advocate of Absolute Monarchy
Actually, Charles was the friend of religious freedom, notably for Catholics. This was met with fury by his opponents!
To be fair, it wasn't quite as simple as that: Catholicism at the time came with a lot of political baggage, including support for absolute monarchy. Charles is certainly guilty as charged on that front.
Cromwell, like Milton, was an advocate, however flawed, of religious freedom and constitutional governemt.
You are seriously confused. Specifically, you are confused between Parliament and Cromwell. Although fighting as a general in the parliamentarian cause, constitutional government's annoying habit of pretending that you have to care what people who disagree with you think was anathema to Cromwell, and he overthrew Parliament in a military coup, introducing an absolutist dictatorship with as little religious freedom as he could POSSIBLY manage.