So Martin Luther didn't get immediatly disowned by the Catholic Church. There was a good year or two where Luther debated with Catholic theologians and officials before he was formally excommunicated by a papal Bull on January 3rd, 1521. About 4 years after he wrote his controversial 95 theses. There were of course theological attacks before that, but the actual secular authorities had no desire to intervene before the formal excommunication.

So Luther was called to the Diet of Worms, which was the meeting of the Electors of the Holy Roman Empire. The electors were the powerful nations that made up the Empire, and were responsible for electing the Emperor. Anyways Luther was tried before the diet and the Emperor, the famous Charles V. Charles V actually found Luther guilty of heresy and placed him under Imperial Ban, the highest punishment the Holy Roman Empire could give out. It made Luther an outlaw, made it a crime to give him food or shelter, banned all his writings, and made it so that he could be killed or captured without legal repercussions.

However Luther got lucky and there was some people willing to protect him from the wrath of the Empire. First off his own religious order gave him theological and legal protection; but far more importantly was the protection of the Elector of Saxony, Frederick the Wise (He built the University at Wittenberg that Luther attended). Frederick was a devout Roman Catholic, and he even disagreed with Luther on a bunch of very key issues. But he was influenced by his secretary Georg Spalatin, who while not really concerned with theological issues was a humanist and sympathized with Luther. Also,sheltering Luther was a way for Frederick to assert independence and test the resolve of the Emperor Charles V, who had only been proclaimed Emperor in 1519. Thus Frederick gave Luther his protection, and had Luther "kidnapped" and put him in a secluded castle called Wartburg castle. This was prearranged by Frederick and kept Luther out of harm's way.

While in seclusion Luther continued his writings, and translated the Bible into German. Other theologians took up Luther's cause and the reformation continued even while Luther was in seclusion. An increasing amount of peasants and princes were embracing the new faith. This meant that many princes didn't want to enforce the ban, and those catholic princes who did, couldn't for fear of a peasant uprising. The Emperor stuck to his guns, fearful that Luther was becoming a rallying cry for Protestant princes to undermine his authority. The Protestants were denied more representation in the Empire's legal and administrative bodies, notably in the Imperial Church where Protestants were heavily discriminated against. As a result Lutheran princes began to form religiously based alliances in order to defend against any catholic retaliation. These alliances tended to be short lived, but they were a forerunner for the religiously based alliances of the Thirty Years War.

The resistance by both Lutheran princes and peasants basically ruled out any chance of striking at Martin Luther violently or having the Emperor forcibly enforce the Edict of Worms on the Lutheran territories where Luther stayed. Had this reformation happened earlier, the Catholic Church probably would have been able to strike Luther down easily. But his new teachings caught on too fast and he found too many powerful allies willing to help him.