Yes, religious differences played some part. But this was largely a political struggle over the Holy Roman Empire (which wasn't Holy, wasn't Roman, and wasn't an empire).
http://www.rockycreekbaptist.org
I have a difficult time defining Catholicism as Christian. The teachings certainly do not coincide with the biblical Christianity I find in the Bible.
And, of course, the Protestant principalities in Germany and elsewhere.
The causes and motives of the wars were, of course, complex -- but religious fervor was a major factor, and also contributed to the ferocity of the killing.
The dynamic of Protestantism vs. Catholicism was a major factor in Switzerland, France, England, and elsewhere. It drove the war between Britain and Spain. It drove the English Civil War.
You simply can't separate religious controversy from much of the conflict in the 16th-17th centuries.