Because of the violence in the medieval times and burning people at the stake a few hundred years ago.
People have been, and always will be, violent. We have a fallen nature. Many persons who have perceived faith in Jesus through the lens of violence misunderstand the essence of discipleship. I point them back to the New Testament, which was written by, for, and about Catholics.
Catholics have committed many aggregious acts. Rejecting Catholicism because of this makes about as much sense as rejecting Jesus because of the actions of Judas and other Jews that rejected Jesus.
I might also show them
where to find the Catechism online or give them a paper copy and ask them to show me where Catholicism is violent.
There is nothing in the Teaching of the Church that enjoins Catholics to be in any way violent.
Why did this happen and what do you say to those who bring it up? (other than “protestants did it too”).
One must understand these things in their context. At the time, heresy was considered treason, as it was a departure from the National Faith. Treason was commonly punished by death.
Nowadays Catholics would condemn it severely I think but I wonder why this happened in the first place (What were the circumstances)
It is very important for Catholics to understand and be able to explain these events in context.
Guess an institution so old is bound to have some dark periods?
It is important to understand that the Church is the Bride of Christ. As such, she is incarnational as He is. She has a Divine part ,and a human part. Jesus is her Head, and she is ensouled by the Holy Spirit. It is these Divine elements that make her infallible, not the human. There are humans attached to the Church who are faithless, and even evil. These persons are not the Source of the Divine Revelation, nor are they good examples of disciples of Christ.
No amount of human frailty can diminish the power of God placed in His One Body, the Church. Many Catholics can sin and do horrible things, but the purity and holiness of God in the Church always triumphs. People have dark periods, and some have dark deeds, but the Light of Christ is always more powerful.
Have any teachings changed since then??
No., but this is a good question to put to your detractors. Can you show me where the Church has ever taught that violence is the way of Christ? If not, then we are talking about Catholics who failed to understand the teachings of Christ.
The burden is always upon the accuser to produce the evidence.