Bohemia in 1600 was overwhelmingly non-Catholic. A century and a half of Hussite history had left the kingdom with its own settlement, and Lutheran and Bohemian Brethren congregations had grown up alongside the Utraquists. The emperor was a Catholic Habsburg presiding over a Protestant kingdom, and he needed the estates far more than they needed him, particularly once his brother Matthias began stripping territories from him.
On 9 July 1609 he signed the Letter of Majesty. It granted the Bohemian estates freedom of religious practice, allowed them to build churches and schools, and put the administration of the non-Catholic church under a consistory and a body of defenders drawn from the estates themselves. As guarantees of religious liberty go in early modern Europe, it was unusually wide, and it was extracted under duress rather than granted from conviction.
It did not hold. Rudolf was forced to cede Bohemia to Matthias in 1611 and died the following year. Under his successors, Catholic officials began obstructing the building of Protestant churches on land they argued was royal and therefore outside the charter, and the estates read that as a breach of the Letter. On 23 May 1618 a delegation of Protestant nobles threw two imperial governors and their secretary from a window of Prague Castle, an act deliberately staged to recall the Hussite defenestration of 1419. All three survived the fall. The revolt that followed became the Thirty Years War, which killed a substantial fraction of the population of central Europe and ended with a settlement, at Westphalia in 1648, that put religious rights on a treaty footing rather than a royal charter.