Yeah, it's all over his poetry and prose. As you're reading Paradise Lost you have to remember at all times lines 22-26 of Book 1, when the speaker (who in my opinion not only /is/, but /has to be/ Milton himself, though it might be argued is a character):
"---- What in me is dark
Illumine, what is low raise and support;
That to the heighth of this great argument
I may assert eternal providence,
And justify the ways of God to men."
This is the summary not just of PL but his entire life project. Going back to "On the Morning of Christ's Nativity," there's a really good article called "Expectation and Prematurity in Milton's Nativity Ode" by David Quint (Modern Philology 97.2 (1999), if you have access to databases and are interested), that analyzes the poem and discovers it deliberately mirrors Euripedes' condensed version of the "Homeric Hymn to Apollo," designed to be an "[o]verturning [of] classical models," and achieve "a purified poetry that separates itself from a fleshly, pagan inspiration" (195). Milton's early concerns with poetry AND community (as opposed to state, I think, and you can see he was Puritan from early on) isn't just that Christianity, in the incarnation of Christ, "[dethrones the] pagan gods," but does not fully do away with them (212). Milton is very concerned with the creeping threat of error: if mankind was able to turn to paganism despite God's lone providence, then surely the birth of Christ doesn't necessarily stop false traditions arising from original (or restored) orthodoxies. It's easy to read here Milton's Anti-Catholicism, but it also has to be read as a criticism of his fellow Protestants- in my opinion, even moreso. This criticism is increased exponentially with the publishing of Samson Agonistes, though that's technically another topic.
What makes Milton as a writer, and Paradise Lost as a work, is not just how encyclopedic he is but how disciplined a thinker he is. You won't agree with everything he says, and sometimes you can see him make very person errors (also interesting), but rarely does he not have strong logic to his arguments. And that's why he continues to go to the classical tradition(s): generally Milton's strategy is to not just present new argument and evidence but to show how, at some point, we took a wrong turn and there's a precedent in the past visibly among Greeks, and Egyptians, and Hebrews, and Anglos, and Romans, and etc. etc. For Milton pagans were wrong to turn away from God but even those that are ultimately in error, including Catholics, can still lead us back to the right track by our own exercise of reason discerning what is true and what isn't. I'm rambling now but the point is Milton's very concerned about the exercise of reason and will and history as a continuum of consequences and conditions.