One reason was technological. Even the two decades between Savonarola's death and Luther's entrance onto the scene saw huge advancements in printing. Through printed pamphlets Luther was able to reach millions with his work when only a generation earlier he would have been safely muffled in an obscure corner of Germany, only heard by those who could hear him speak in person.
Another reason was location. Savonarola was in Italy, practically in the Pope's back yard. Luther was up in Germany, further away and protected by the complicated politics of the time. Frederick III, Elector of Saxony, was one of the most powerful German princes and kept Luther under his protection against both Pope and Holy Roman Emperor Charles V, allowing him to continue his work with relatively little fear. While it does not seem he was ever very enthusiastic about Luther's doctrine, he had political reasons for defying Pope and Emperor, and also valued Luther as the star professor at his new university at Wittenberg, only established in 1502. Frederick was succeeded in 1525 by his brother John, who was himself a devout follower of Luther by that time.
Finally, Savonarola advocated certain positions far more extreme and apocalyptic than Luther ever did. Luther, especially after the 1525 Peasants' Revolt, had a very high view of civil order and the God-given role of the government in maintaining peace, as he explained in discussing the doctrine of the Two Kingdoms. Savonarola, on the other hand, took a view more similar to the later approach of Calvin in Geneva, claiming a theocracy in Florence and threatening to severely upset the balance of earthly power. While Luther's work certainly had political implications, Savonarola posed not only a religious but also a political threat in a way Luther never did.
Kolb, Robert. "'Saint John Hus' and 'Jerome Savonarola, Confessor of God': Lutheran 'Canonization' of Late Medieval Martyrs". Concordia Journal vol. 17 no. 4, October 1991.
Porter, J. M., ed. Luther: Selected Political Writings. Fortress Press: Philadelphia, 1974.
Weinstein, Donald. "Savonarola, Florence, and the Millennarian Tradition". Church History vol. 27 no. 4, December 1958.