Well, obviously there is not an 1-1 similarity but 16th century was not a good time for religious tolerance. It was a time of inquisition, witch hunt, reformation and counter-reformation, wars of religion and book burnings everywhere.
Maybe more robustly in a bit, but suffice it to say, "witch hunts" were heavily localized, and not particularly common, deadly, or persistent even in the regions in which they did occur (and were also largely a 17th century phenomenon). Degree of religious tolerance varied heavily by region, type of settlement, ruler, and time period. Reformation and counter-reformation doesn't really say anything about violence and intolerance
per se. Book burning/banning was, again, nowhere near as commonplace or widespread as you seem to think it was.
This was also the period in which humanism exploded into the political conscious. The 16th century was the first time where, on a large scale, knowledge, learning, and the arts were being weaponized as tools in political warfare. Learning and the arts were exalted by secular leaders to a degree that hadn't been seen in that way in hundreds of years. The reintroduction of Greek was an enormously costly, generations-spanning endeavor. We're talking on the level of billions of dollars in today's terms. Latin scholars were finally reading things other than Cicero and Boethius. For the first time, again, in centuries, people were going into Monastic libraries and taking books off the shelves. The Renaissance wasn't about the rediscovery of classic texts in that Western Europeans discovered that Muslim and Orthodox scholars had been preserving them all this time, so much as it was a discovery that
Western Europeans had these books all along, but nobody was really looking for them. I can't remember the specific text (might have been
De Rerum Natura) was discovered literally being used to hold up a table. It had probably been serving that purpose for several hundred years. The only extant copy of that text, and nobody had bothered to look at it until then.
Christianity in this period also changed profoundly. Firstly in the introduction of humanism into Christian theology, and secondly due to the emphasis on spiritualism. Christianity, on the whole, in this period was one concerned far less with slavish concession to authority, and one much more concerned with experiential spiritualism. Anybody who would characterize the 16th century in such a way as you have has clearly not read Erasmus or Teresa of Ávila or Savonarola. Hell, or even the major Reformation figures like Luther, Zwingli, Melanchthon, or Bucer. There was far more to it than you seem to think.
I won't say it was all sunshine and roses. I'm not delusional. The Peasants' War, the
Beeldenstorm, and the Italian Wars were all horrific and destructive, to say nothing of the violence perpetrated against the Jews at this time. But there was also a ton of good that was happening at the same time. It was a beautifully complex era in a beautifully complex region. It's like, the main reason why I study it.