That's an over-simplification; there are examples of Hapsburg monarchs being anti-Protestant, and examples of them being not-anti-Protestant (Austria itself was majority-Protestant at one point, for example, and the Hapsburgs were able to rule over it without alienating everyone).
ETA: Plus, it was Ferdinand II personally whose anti-Protestantism caused the Thirty Years' War, not the Hapsburgs' in general; the Emperors before him were quite tolerant, and managed to largely keep the peace in difficult circumstances. Plus plus, the policies of the Hapsburgs in the seventeenth century aren't necessarily a good guide to what their policies in the nineteenth century would be like. A lot can change in two hundred years; for example, the US in the nineteenth century had a "pretty extreme" history of being pro-slavery, but the same certainly can't be said for the US today.
Not to mention you could have tolerance change even between two rulers. You had Maria Theresa who was very devout and then Joseph II whose attitude towards religion was certainly more pragmatic.
Although I guess Austria's reputation during the 19th century is mostly due to Franz Joseph being around for very long, and even then he was only ruler for half of said century (he did have Franz I as a grandfather, who certainly was more Maria Theresa than Joseph II).