One of the main causes of persecution is intolerance, something the Catholic (C)hurch has a great deal of experience with. They've been using it for centuries. Ask Galileo.
What was it about the Pope's statements indicated intolerance? There was no intolerance in his statements.
As for Galileo, the Church was tolerant and patient with him and he was tried for attacking the Pope who was supporting him. Galileo was imprisoned in his own home and was treated well for disobeying the Pope who was his friend. It turns out that the Church was correct on the science that Galileo was only half right.
Yes, the Galileo story is quite a bit more complicated than 'The Church was angry and anti-science and was MEAN to Galileo' which is what many people believe. Keep in mind that the first describer of heliocentrism, Copernicus, was in fact a Catholic monk.
Galileo's work was sponsored by the Church and, as was the common practice of those days, Galileo went to talk to his sponsor about his plans to write a book based on his discoveries. Now, Galileo wanted to make a book that simply declared that heliocentrism was correct, and didn't mention geocentrism at all. The pope told him that he should instead write his book in the Socratan style (i.e., Socratic method) (the most common style of the day) as a dialogue between someone who supported geocentrism and someone who supported heliocentrism. Galileo agreed.
Fast forward a year or so and the book is published. Sure enough, it is a dialogue between geo/helio-centrists. But there's a problem. See, Galileo wasn't exactly the most... tactful... person, and he was kinda annoyed that the pope had told him to write it in this style. So when people read the book, the geocentrist, named 'Simplissimus' (Simplicio), was a bumbling buffoon (which would have been okay), whose facial features matched the pope and whose choice of words and phrases matched the pope as well. Galileo was libeling the Pope.
It is this libel, the depiction of the pope as an idiot, which got Galileo in trouble and got his book banned. His science, which had been supported by the Church for years, wasn't really a problem.
A colleague was surprised to learn the facts about Galileo's behaviour over a recent dinner conversation. The colleague, who began to spout the usual litany of complaints against the Church before I seeded the conversation with a remark about Galileo's problematic presumption, had bought into the tabloid version of events massaged into her brain by who knows which media organization's limp "news" articles and/or other casual conversations founded on nothing more than lazy thinking.
"The Bible shows the way to go to heaven, not the way the heavens go."—Caesar Cardinal Baronius, contemporary of Galileo Galilei. The quote is often wrongly attributed to Galileo.