Throughout history there have been many intellectual arguments for and against Christianity, often debated by some of the greatest minds in the schools of philosophy, history, theology and apologetics. Entire books have been written discussing these arguments, by Christians, Atheists and people of other ideologies. Many of these arguments, both for and against, are very well thought out, extensively explained and could represent good reasons to either accept or reject Christianity as truth.
Unfortunately, most people in our society today couldn't think of even one of those arguments if their life depended on it.
Instead, one of the most common alternate approaches that anti-Christian bigots like to use is to bring up one of the arguments from what I call the "Naughty Christians" pantheon. These are arguments which all share the similar trait of claiming that Christianity is wrong because some group of people who were supposedly nominally "Christian" did something bad. And three of the most common appearances from this pantheon are the Crusades, the Witch Trials and the Spanish Inquisition. As is often the case with ignorant arguments against Christianity, these arguments are wrong from both a rhetorical/logical standpoint, as well as having serious factual shortcomings. We will briefly cover the factual shortcomings first.
But brings us to the rhetorical and logical problems with these arguments. As is very often the case with arguments from the "Naughty Christian" pantheon of arguments, these supposed "evil deeds" that are being attributed to all Christians everywhere were actually carried out almost exclusively by Catholics in Europe. As I've pointed out many times before and will continue to point out as often as needed, Catholics and Protestants aren't following the same religion. Although this claim is often challenged, it is objectively true and agreed upon by both sides from a purely canonical standpoint. The Roman Catholic Church officially issued 100 anathemas (curses) against all Protestants everywhere, effectively stating that Protestants aren't "real" Christians and that until we submit to their authority we are all going to hell. Conversely, the whole concept of being "Protestant" is that you are protesting something, namely the Catholic Church in the case. So there is absolutely no argument to be made that Protestants and Catholics are part of the same group. Catholics and Protestants are explicitly enemies. Blaming Protestants in America for the actions of Catholics in Europe would be just as ignorant as blaming Franklin Roosevelt for the actions of Adolph Hitler. It makes no sense at all.
So even if you want to ignore the factual shortcomings of the Crusades, Witch Trials and Spanish Inquisition as arguments, then you must at least admit that the party truly responsible for these deeds was the Roman Catholic Church. In which case you should join Protestants in calling out the Catholic hypocrites, not try to demonize us along with them.