I know that before the Protestant revolt, basically all of Europe was Catholic and the Church had lands and money coming from all sides, but even then, things were not 100% all sunshine and roses. Over and over again, kings would try to usurp the rights of the Church and impose their nonsense or demand money etc. There was always some trouble or another, even in the most Catholic of times, and even when kings were "Catholic," they still opposed and hurt the Church in various ways.

So why were kings "afraid" of the Church and regarded Her as too powerful if, in the end, they always had their way and were always bossing the Church around? As far as I can tell, the Church has never had an army and never went around conquering or threatening war and conquest, so I don't think there was any sort of fear or danger from kings of being "conquered" or attacked by the Church/Pope.

From what I've seen, most kings and nobles were wicked and Catholic in name only, so I don't see why they feared being excommunicated so much if it didn't mean anything for them in the practical world.

We saw how Henry VIII went ahead and split from the Church in the end, excommunicated and all, along with all the other heretics.

So what was the practical consequence of being against the Church and being excommunicated?

I just saw the movie Bekcet and read about St. Thomas Becket, and I don't understand why Henry II feared the Church so much if, in the end, he got St. Thomas killed and did what he wanted anyway.

It was rather rare for a King to openly defy the Church, it's just that usually those figures are more famous than the ones who didn't. They were terrified of excommunication, and there are many paintings of Kings lamenting their excommunications with great sorrow. 

Anyway, Kings did not always have their way. Every time a King defied the Church, there were almost always nobles within his realm or without who would defend the Church. The Pope won out in the Investiture Crisis in both England and the Holy Roman Empire, in England by peace and in the HRE by cινιℓ ωαr. Two major victories for the Papacy.