Why did Holy Roman Emperor Rudolph II reverse his father Maximilian II's tolerant policy toward Protestantism?
Maximilian had a strong protestant influence from his environment. RII didn't have this. Also the various wars in this time played a strong line.
F.e. when they needed alliances against the Ottomans they would grant the protestants some freedom, but take it away, when they didn't.
Also I know the Catholic church is said to be mostly at fault nowadays, but believe me the other side were also no angels.