Yes. And then they stopped just pointing the guns, started firing them and butchered each other with wanton abandon. The later 1500s and early 1600s are not without reason known as the time of the wars of religion. Just because it may seems like 2 things are very similar doesn't mean that tiny insignificant detail isn't going to lead to massive conflict.

Religion was incredibly important at the time, it infused every part of society in a way we probably have difficulty understanding. It was not just a personal matter, and what the people around you did mattered to your immortal soul too. You could be damned by the actions of others and if you suffered heretics around you well god's wrath would come down on you all. If the pope placed your country under interdict well sucks to be you when you go to hell because the king was lecherous bastard not following what the pope said. Now it's not just about papal authority, many Catholic kings could have joined that bandwagon. The problem was that a large share of Protestant reformers wanted to do away with much of the Catholic church's established authority, wealth, practice and influence as being later additions to the "true religion". The idea to sell absolutions to people is something of a poster child of the things many could see was blatantly opportunistic. There were fairly important questions reaching deep into the societal body which were being changed.

Protestantism wasn't a monolith either, e.g. the followers of Calvin and Luther was as vary of each other as they were of the Catholic majority, and often preferred dealing with them instead, e.g. the Peace of Augsburg in 1555 only covered Lutherans (as there were Lutheran princes negotiating), but not Calvinists. Protestantism also spread in patches and streams as and when influential people moved around and it was quite successful being embraced by many of what for want of a better term could be called the "middle class" of the era, workers and artisans in the towns, but also among nobility and clergy (several bishops and even a cardinal turned protestant). So you end up with patchwork of protestants normally surrounded by Catholic majorities in most of Europe north of the alps and Pyrenees. We could generally say the further north the more successfully with England, Denmark-Norway and Sweden turning officially protestant along with several important German principalities.

Since states were much weaker and less loosely administered such spots of upheaval could have far ranging results. The German Peasant's War 1524-1525 was influenced by reformation ideas and soured the upper tiers of society on the whole thing even though e.g. Luther sided with the authorities (he was a big fan of order in society). Several other short conflicts with part religious causes erupted in the period leading up to the 1600s. The most violent were the French Wars of Religion 1562-1598 which degenerated into a series of religious civil wars with massive atrocities. With printing presses widely available it was possible to diffuse sensational and salacious news like this. If it bleeds it leads, even in the 1600s. Pure propaganda was also an active ingredient demonizing the other side.

So basically the state of relations between Protestant and Catholic was relatively bad in a general sense going into the 1600s. Protestants would have felt, and rightly so, under siege from the Catholic majorities. And Catholics had ample proof of how violent and insurrectionist these fanatics could be. The Peace of Augsburg managed to control such things in the Holy Roman Empire for a while until the succession crisis of Bavaria in 1618 erupts into a conflict that gains religious overtones and draws more and more polities into what becomes the 30 Year War. During the war countless atrocities occur, again widely distributed propaganda tells people how evil the other's are. Though for most people on the ground it turns out it doesn't matter so much whether the soldiers or you are Protestant and Catholic all the woes of war follow anyway.

That's a general sense, on a more ground level the religious differences didn't need to be so implacable. And many people were in a personal sense much more flexible in whether they identified as Catholic or Protestant depending on where the best interest lay, whether soldier or upper nobility. A mixed community would probably be more concerned by the outside soldiery, regardless of their religion. We also have examples of people who just wanted everyone to get along like Michel de l'Hôpital, French chancellor presiding over some of the most lenient Edicts issued in France and Michel de Montaigne a French humanist of the period who, though Catholic, was friendly towards protestants too.

Following the Peace of Westphalia in 1648 it's probably fair to say religion and the Protestant/Catholic divide was less prevalently used as an excuse to go to war. And relations probably improved generally, people would not necessarily be killed for their beliefs. Though rhetoric like the "Papist threat" continued to be exercised. It's not until the Age of Enlightenment we get to point where religion starts to become a matter for the person and not society. Many people who are of the "wrong" religion for their nations are allowed or encouraged to emigrate in the 1600s (thus countries tended to homogenize in religion during the period) under the principle established in the peace of Westphalia that the prince of a realm could decide what religion the country was. However there was a provision of you were in private, and limitedly in public, allowed to worship your non-majority denomination. This gave a legal framework for relations between different communities so at the ground level you have less tension between the groups.

I would be remiss to note that many other factors tied into the relations between Protestants and Catholics. Much of the problems in the French wars of religions came from a powerful noble family taking the last weak Valois French kings under their control and using religion as a tool for political advantage. Not to mention England, Denmark and Sweden all suffered from succession and political crises partly influenced by religion. So relations tend to fluctuate depending on time and place.