I was under the impression that Bohemia was pretty Protestant until Austria Counter-Reformationed it. So if you get an independent Bohemia, it could work. I'm a bit fuzzy on the details, but a good time for this would probably be around the 30 Years War.
I was actually thinking of writing a timeline a while back about Protestant Slovenia, since IIRC they went majority (or at least significantly) Protestant right after the Reformation, and stayed that way until Austria pushed the Counter-Reformation and expelled the Lutheran preachers. So to avoid their re-conversion to Catholicism, you basically need them to be independent from Austria. Unfortunately, due to the geographical size and position of Slovenia (it's small and was considered to be part of the Austrian Crownlands), not to mention the fact that there's very little arable land, and there really isn't a good way for them to gain independence. The other option is to have someone else take over Slovenia, the two principal suspects being Venice and the Ottomans (hey, it worked for the Protestants in Ottoman Hungary!).
The problem with the Ottomans taking it is that it's at the very edge of their territory, it's not very good land, and it's close enough that the Austrians are going to be furiously trying to get it back. But I could see it becoming something similar to the Croatian Military frontier, where Austria promised freedom of religion to anyone who was willing to settle there and fight the Ottomans.
Venice at this time period I don't know so much about, but I would assume they would be interested at least in the coast. Which would of course once again get the Austrians upset since Slovenia was their main access to the Mediterranean.