Cromwell's prejudices were a relative novelty. As far as the Tudors were concerned, they'd bent over backwards to satisfy the local Irish potentates. It said as much about their poor comprehension of the country as anything else, but they in no way regarded Irish people as innately inferior; to them it was all a sort of kulturkampf. See, e.g. Thomas Butler, a personal friend of Elizabeth I.
Thomas Butler and much of the Irish aristocracy despite the whole "more Irish than the Irish" thing were still regarded as Englishmen who had gone native and needed to be "reclaimed" and re-Anglicised, as such you are right the Tudors did bend over backwards in order to get the Old English aristocracy to assimilate. As for views of the actual natives it was a long period with a huge number of individuals involved and often contradictory policies so you can find evidence for pretty much anything between sweetness, light and respect for Gaelic Catholicism to the opposite extreme. However there was a clear policy of turning Ireland from a land inhabited by Gaelic speaking people to one inhabited by English speaking people, it wasn't just a religious thing because why else would the Catholic Mary carry out the first Plantations?
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