Paradise lost was not seen as sympathetic towards Satan until the Romantic era. It was Blake who said that Milton was "of the Devil's party without knowing it", at the time a radical reinterpretation, but with emphasis on "without knowing". Milton was a devout Christian and though the text is can be seen as subversive from a post-romantic, rugged individualism perspective, the original religious intent is made clear from the beginning, "to justify the ways of god to man". However, as recently as 1941, CS Lewis wrote that the poem does not seek to glorify Satan:

In the same way, the proposition that Milton's Satan is a magnificent character may bear two senses. It may mean that Milton's presentation of him is a magnificent poetical achievement which engages the attention and excites the admiration of the reader. On the other hand, it may mean that the real being (if any) whom Milton is depicting, or any real being like Satan if there were one, or a real human being in so far as he resembles Milton's Satan, is or ought to be an object of admiration and sympathy, conscious or unconscious, on the part of the poet his readers or both. The first, so far as I know, has never till modern times been denied; the second, never affirmed before the times of Blake and Shelley-for when Dryden said that Satan was Milton's 'hero' he meant something quite different. It is, in my opinion, wholly erroneous. In saying this I have, however, trespassed beyond the bounds of purely literary criticism. In what follows, therefore, I shall not labour directly to convert those who admire Satan, but only to make a little clearer what it is they are admiring. That Milton could not have shared their admiration will then, I hope, need no argument. The main difficulty is that any real exposition of the Satanic character and the Satanic predicament is likely to provoke the question 'Do you, then, regard Paradise Lost as a comic poem?' To this I answer, No; but only those will fully understand it who see that it might have been a comic poem.

In terms of whether this intention resonated with contemporaries, Maltzahn reports that "the conservative Hobart welcomes Milton's christian epic as a counterweight to the irreligious court culture of the day". He goes on to discuss the contemporary need to separate Milton's incendiary political views from his orthodox religious ones. Paradise Lost was controversial when seen as a political allegory, depending on which side of the English civil war you were on. As CS Lewis mentions, Dryden handled this topic as well, and as a royalist he rewrote the poem figuring Satan as Oliver Cromwell, which was certainly meant to be an insult not a compliment.

In terms of Milton's sensitive publications, his Aeropagitica is a polemic arguing for free speech. This and his discussion of divorce were the publications which attracted the most controversy although they were never censored. Remember that this is well after the reformation, and though it might be a generalisation, power lay with either the King or parliament, not with the church. If something was politically expedient it was allowed, see Christopher Marlowe's extremely blasphemous productions of Doctor Faustus while allegedly in the secret service of Elizabeth I.

Sources:

Alicia Ostriker, Dancing at the Devil's Party: Some Notes on Politics and Poetry Critical Inquiry Vol. 13, No. 3, Politics and Poetic Value (Spring, 1987), pp. 579-596

C. S Lewis, A Preface To Paradise Lost (London: Oxford University Press, 1942).

John N King, Milton And Religious Controversy (Cambridge: Cambridge Univ. Press, 2001).

Nicholas von Maltzahn, The Review of English Studies Vol. 47, No. 188 (Nov., 1996), pp. 479-499.

William Blake, The Marriage Of Heaven And Hell And A Song Of Liberty (New York: Florence Press, London, 1911).

OP, you might consider x-posting this question to /r/AskLiteraryStudies for their perspective

During and after the civil war (a period that Milton lived through), there was a huge outbreak of politico-religious experimentation and unorthodoxy. The classic study is Christopher Hill 1972, The World Turned Upside Down: Radical Ideas During the English Revolution. New sects sprang up like the Levellers, the Diggers, the Ranters, the Quakers, Fifth Monarchists, Grindletonians, Muggletonians etc etc. Many of these groups did not believe in life after death, or the historical Christ, thought the Bible was mainly allegorical, and subscribed to a general rationalistic "pantheism", which we would probably call atheism by our standards. Gerrard Winstanley, a Digger, equated ‘God’ with ‘Reason’; a Ranter, Laurence Clarkson, wrote that to the truly pure, ‘Devil is God, hell is heaven, sin holiness, damnation salvation’ (A Single Eye, 1650). Milton actually said something similar in Aeropagitica: ‘To the pure all things are pure, not only meats and drinks but all kinds of knowledge, whether of good or evil.’

So there were a lot of these ideas around during the interregnum, driven as explained in another comment by a relaxation in printing censorship, and it's a key part of the intellectual environment that continued even after the restoration specifically through writers like Milton and Bunyan. In many ways, his religious thinking, though often radical, wasn't especially unusual for his period: what's unusual is that he's become enshrined (with reason) as a canonical Great Writer, whereas most of his contemporaries with similar ideas have long been dismissed or forgotten as minor heretics or pamphleteers.

If you want to get more into this, Hill's book includes an appendix dedicated to Milton and how he contributed/reacted to the religious experimentation of the civil war period.