We need to go a little back in time to understand what was the political climate in The Lands of the Bohemian Crown at the beginning of the 30-Year War. TLotBC were predominantly non-catholic at the beginning of the 17th century. It is more precise to use the term "non-catholic" rather than an encompassing term "protestant" because the religious scene was pretty diverse, there were utraquists here, lutherans, calvinists, the then-banned Unity of the Brethren, etc. and these groups had their own agendas, sometimes in conflict with those of other non-catholic groups.

The Letter of Majesty (1609) issued by Rudolf II. allowed for freedom of religion for catholics as well as non-catholics and adressed their relations. It helped to relieve some religious tension in Rudolf's lands. Somewhat. For instance, the High Chancellor Zdenko Adalbert Popel von Lobkowitz, a bigot catholic, refused his duty to sign The Letter. The High Burgrave Adam II. von Sternberg, a moderate catholic, had to sign The Letter in his place. Since 1611 when Rudolf was forced to give up the Czech Crown in favour of his brother Matthias, tensions gradually arose again because Matthias intended to strenghten the position of catholics and pretty much didn't care about legal bindings of The Letter. Matthias moved his seat from Prague to Vienna and no Habsburg successor ever returned the seat back to Prague.

If Matthias was "moderately annoying" to non-catholic nobility, then his successor Ferdinand II. was a total "red flag" for them, although they realized too late. Ferdinand was elected by The Bohemian Diet to be the next Czech King in 1617 on condition that he would honour The Letter. Which, he did not intend to. Soon after the election, he took matters firmly in his hands despite Matthias, old and ill, still formally being the king of Bohemia until his death in 1619. This was one of major factors of why did the 30-Year War start in 1618 and not later.

All those previous tense years also mean that the defenestration of 1618 was no random impulsive act. It was a thoroughly planned act and in the minds of the rebels it was even a rightful act in the tradition of earlier Bohemian defenestrations where law-trespassing officials were punished. And, uh, yeah, there were possibly also less noble motives behind the plan, like lucrative titles. One of the coolest castles in Bohemia was Karlštejn and its Burgrave job was very prestigious and well paid. One of the soon-to-be defenestrated guys, Wilhelm Slawata von Chlum und Koschumberk, was the Burgrave of Karlštejn until 1611. Then a power struggle played out in Bohemia and he was replaced by Heinrich Matthias Graf von Thurn und Valsassina who held the title until he refused to acknowledge Ferdinand II. as the new king. Von Thurn was then replaced in the Karlštejn Burgrave office by Jaroslav Borsita von Martinitz, the second soon-to-be defenestrated guy. Von Thurn was a key rebel figure who co-orchestrated the defenestration and actively participated in its execution. Out of all king's representatives present in the office that day only these two were thrown out of the window (and their scribe who wouldn't shup up). What a coincidence. In any case, the defenestration served to incite anger and unity among non-catholic nobility. Although the rebels wrote a letter of apology the very next day after the defenestration, stating that they merely wanted to punish unworthy officials, this move couldn't realistically prevent a war with Ferdinand and rather served as the casus belli to attract foreign help.

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Fastforward to the defeat of rebels at the Battle of White Mountain.

We need to remind ourselves here that Ferdinand II. faced the 30-Year War and had serious trouble to solve at a much larger scale beyond the borders of TLotBC. He had to solve domestic unrest at a reasonable pace and in the meantime to keep his international war efforts funded. If his trouble was only Bohemia, he would merely behead the rebel leaders, appoint new officials, issue a law or two to cement his catholic agenda and then force these to come into effect, all of that during 1621.

Instead, the process was rather a slow one (for Ferdinand's tastes, that is), gradual and had to acknowledge rewards for foreign power players who helped Ferdinand II. to consolidate his lands. From a religious point of view the recatholization process was too fast, too forceful and resulted in a persistent resistance against these efforts. Overview of important events:

1621: 10 days after the Battle of White Mountain, Maximilian I., Elector of Bavaria, appoints catholic Karl von Lichtenstein as Ferdinand's representative for Bohemia administration. For Moravia, bishop cardinal Franz von Dietrichstein is appointed.

1622-1623: A secret financial group, the so-called Prague Coin Consortium is established to handle difficult income/expense issues for Ferdinand II. They lend Ferdinand a whopping 6 millions of guldens in exchange for 14 months lasting control over all the mints in Bohemia, Moravia and Lower Austria. They also gain rights to perform a monetary reform. They operate akin to present day mafias - they coin new coins with 8x lower share of silver, they manipulate sales of rebel property, vastly enrich themselves and cause state bankrupcy without ever being accused and punished. When the crisis is resolved, new coins are worth 1/10 of old value, impoverishing most people of all social classes.

1624: The Czech Court Office moves from Prague to Vienna.

1627 (Bohemia) / 1628 (Moravia): The new constitution is published and forced into effect without required confirmation by The Bohemian Diet. Published fully in German under the name "Verneuerte Landesordnung". The Czech version wasn't even fully published. The new constitution was essentially a foundation stone of monoreligious absolutism and germanisation. Catholicism was not only promoted, Catholic Church representatives were also given much more power in The Bohemian Diet. Nobles in The Bohemian Diet, on the other hand, were severely limited in their voting power and royal cities were made almost voteless. German language was added as an official language in TLotBC, formally equal to Czech, in practice though, German was made superior to Czech.

1627: Ferdinand II. issues a mandate that orders non-catholic nobles to either convert to catholicism within 6 months or to go into exile.

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Here's an overview of key Ferdinand's representatives in Bohemia after the Battle of White Mountain.

Governor of Bohemia

1621-1627: Karl von Lichtenstein

Governor of Moravia

1621-1628: bishop cardinal Franz von Dietrichstein

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Then there was The Royal Council of Bohemia which consisted of twelve members. There were some adjustments made to these ranks after the introduction of the new constitution of 1627. Nothing important for the scope of this overview though. Here's the six most important ranks out of the total twelve, sorted by their importance/power.

The High Burgrave of the Kingdom of Bohemia (chairman of The Bohemian Diet, the head of the Prague Castle and the military leader of the land's noble armies)

1620-1623: Adam II. von Sternberg

1623-1627: vacant

1627-1638: Adam von Wallenstein

The High Hofmeister of the Kingdom of Bohemia (the head of king's advisors, the head of court justice)

1620-1627: Adam von Wallenstein

1627-1628: Wilhelm Slawata von Chlum und Koschumberk

1628-1638: Jaroslav Borsita von Martinitz

The High Marshall of the Kingdom of Bohemia (executive head of The Bohemian Diet, court justice responsibilities especially in regard to honour cases of nobles)

1620-1626: Lev Burian Berka von Dubá

1626-1644: Matyáš Ferdinand Berka von Dubá

The High Chamberlain of the Kingdom of Bohemia (court justice responsibilities especially in regard to criminal and property cases of nobles)

1618-1623: Jiří von Talmberg

1623-1625: Wilhelm Slawata von Chlum und Koschumberk

1625-1628: Jaroslav Borsita von Martinitz

1628-1638: Fridrich von Talmberg

The High Judge of the Kingdom of Bohemia (preparation and leading of court cases in regard to criminal and property cases of nobles)

1620-1624: vacant

1624-1625: Jaroslav Borsita von Martinitz

1625: Fridrich von Talmberg

1625-1627: vacant

1628-1638: Heinrich Liebsteinsky von Kolowrat

The High Chancellor of the Kingdom of Bohemia (an official responsible for proper legislative of issued laws - his signature was required along the king's signature)

1599-1628: Zdenko Adalbert Popel von Lobkowitz

1628-1652: Wilhelm Slawata von Chlum und Koschumberk

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Unofficial power structure (1622-1623):

Prague Coin Consortium

Karl von Lichtenstein

bishop cardinal Franz von Dietrichstein

Pavel Michna von Vacínov

Albrecht von Wallenstein

Hans de Witte (a Dutch calvinist financier)

Jacob Bassevi von Treuenberg (a Bohemian Court Jew, noble and financier)

+10 more unknown members

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Sources:

Petr Hora-Hořejš: Toulky českou minulostí, part 3 (in Czech)

TV talkshow Historie.cs, part "Dveře všech běd", with historians Václav Bůžek, Jiří Mikulec, Klára Andresová (in Czech)

Robert Bireley: Ferdinand II, Counter-Reformation Emperor, 1578-1637 (in English)