The Bohemian crisis is usually regarded as the start of the Thirty Year War.
1. The Defenestration of Prague was symbolic that all was not well in the empire and that absolute rule did not exist. The basic issue was who ruled Bohemia - the nobles? the Estates? or the emperor? If Ferdinand re-asserted his power in Bohemia would he feel confident enough to try the same in Germany ? What would the reaction of the north German princes be to this ?
2. After the Battle of White Mountain, what happened to Bohemia ? Could this be an example of what would happen to north Germany if Ferdinand tried the same ? What would happen to the Electors land if they opposed Ferdinand when the example of Frederick's treatment after White Mountain is taken into account ? If Ferdinand was willing to do this to the most senior of Electors, what about the 'weaker' ones ? Did Ferdinand have the right to dole out at will Electoral land ? Did he have the right to confiscate Electoral land ? There may have been a legal right for Ferdinand to do this (as Frederick was guilty of leading a rebellion), but the other Electors and princes would not have supported this whether it was legal or not.
3. A secure Catholic block in the Palatinate was a direct threat to the region that was mainly Protestant. A Catholic Palatinate was near to Catholic Spain (ruled by a Habsburg) and relatively near to Catholic Bavaria. France, regardless of being Catholic, saw this as a direct threat to her and fears of Habsburg encirclement once again reared its head in Paris. By 1620, France was relatively stable internally and she could involve herself in European affairs if she needed to.
4. The Palatinate gave Spain the opportunity to move troops north to the Obedient Provinces (those parts of the Spanish Netherlands that had remained loyal) and threaten the United Provinces. This could only increase tension in northern Europe. England and Spain would not have tolerated any Catholic presence in the north of Europe.
The German princes had had nearly 100 years of effectively governing themselves after Luther published his 95 Theses. This era of effective self-government was all but free from Imperial interference and witnessed a time when the rule of the emperors was seriously eroded. The princes had got used to this self-government but to a man who believed in absolute rule of his territories it was completely unacceptable.