In 1618 years of conflict between the protestant Bohemians and the catholic Habsburgs, house of the Emperor of the Holy Roman Empire since 1438 and the kings of Bohemia since 1526, erupted in a rebellion that marked the beginning of the 30 Years' War.

The Bohemians demanded retention of Freedom of Religion and of the rights of their 'Landtag' ('estates') while Emperors Matthias, who died in 1619, and Ferdinand II, his successor, were all about Counter-Reformation and centralization.

The Bohemians elected protestant Elector Palatine Frederick V as their king, who garnered the support of the alliance of important protestant german princes called 'Union'. In 1620 the Bohemians lost the decisive Battle of White Mountain just outside Prague and Frederick V had to flee. After some sabre-rattling by emperor Ferdinand II the Union dissolved itself in exchange for neutrality.

From now on Ferdinand II started with a systematic program of disenfranchisement of Bohemia, culminating in the so called 'Verneuerte Landesordnung' (~ 'renewed constition') in 1627, that made the crown of Bohmeia hereditary to the House Habsburg, deprivated the bohemian Landtag of most of its rights and made protestantism, even that of germans who had immigrated into Bohemia after the Hussite Wars, absolutely illegal. Jesuits flooded the country and garnered control of the education, and whoever wanted to stay protestant had to leave.

Not all protestantism ended in 1627, but in the long run it would.

Sources:

C. V. Wedgewood 'The Thirty Years' War'

Mann, Golo 'Wallenstein'

Barudio, Günter 'Der Teutsche Krieg. 1618 - 1648'