Las Casas' work criticizing the encomienda system had many supporters, at the same time there were significant adversaries against Las Casas. These detractors fell among two lines: first are those whose interest lie with the encomienda system at it was, and second are those who insisted on the righteousness of the cause of the encomienda system.
To fully understand the second, and how the encomienda system arose, we should note that this system was adapted from one used during the reconquesta, whereby military orders were granted temporary grants of land recently captured from the Moors. In the Americas, the encomienda was not a landed estate system, rather the encomendero was obliged to instruct the natives into Christianity, and in return he could get their service and tribute. Prior to this, the natives were sold outright into slavery, until such practice was banned under Isabella and Ferdinand. One argument was that native Americans had not previously been exposed to Christianity, so therefore they deserved instruction so that they would accept Christianity. The encomienda system was put in place with this in mind, and therefore in theory had very strong alignment with Spain's religious character. Of course, we now know that it was nowhere near the peaceful and mutually beneficial system that it sounded like in theory!
When Las Casas first took up his cause in Spain in the 1510s, it took a very long time for his specific ideas to be formed, and for them to gain traction. So, one may ask, why did it take decades for the ideas to be accepted? Unsurprisingly, it had to do with politics. Las Casas' first mentor was Cardinal Ximenes/Jimenes Cisneros, confessor of Isabella and later regent of Castile. Cisneros thought Las Casas was too radical, even if he was in agreement with the Humanist views. When Cisneros passed away, Las Casas was able to gain the support of the Flemish party in Charles V's court. He knew that he needed a proposal of how to reform or outright replace the encomienda system, many of which were poorly implemented and failed miserably. Among other things, he advocated settlement of Castile's peasants and importation of African slaves, which I won't get into too much detail here. Further, over time his Flemish supporters either passed away or were caught in the Revolt of the Comuneros.
One primary opponent of Las Casas was Sépulveda, a strict Aristotelian, who was a champion of the idea of "natural slavery," justified by the inferiority of the native Americans (and other groups of people). He was not just a scholar, he was Philip II's tutor before Philip came of age. The arguments came to a head in a famous debate between the two in Valladolid in 1550, which itself is testament to the vigorous intellectual tradition at the time even if it had taken Las Casas decades to secure that opportunity.
Contrary to expectation, the debate wasn't a resounding victory for Las Casas. Fortunately, at the same time, at the highest royal circles there was already a shift toward more humane treatment of native Americans. So while Las Casas deserves great credit, so do royals such as Charles V and Philip II.
So, was there no progress over the decades between Las Casas' first publication and the debate of 1550? As time neared Las Casas' debate in Valladolid, there were already many regulations that improved treatment of native Americans. Enslavement under any condition was prohibited in 1530. The law reforms of 1542 strengthened requirements for slave-owners to claim ownership of slaves, the same year as the publication in question, although I do not know which came first. Finally in 1549, it was forbidden to substitute forced labor in place of payment of tribute. All these decrees and reforms came even before the debate in 1550.
Of course, the implementation of the decrees took a long time, given that this was the 1500s and communication/control of the monarchs over their far-flung dominions were very limited. Further, many were pragmatic regulations, seeing that so many native Americans have died that they had to change the system. So clearly, the ever-lasting struggle for control between the crown in Spain versus its agents in the New World played a big part. Therefore, while Las Casas was an important leader, and deserve credit for framing the cause in terms of humanism, his cause strongly benefited from the ongoing struggle for control, which in the end dismantled the encomienda system.
Sources:
J. H. Elliott, "Imperial Spain: 1496-1716," ISBN-13: 978-0141007038, 2nd ed 2002.
H. Kamen, "Spain's Road to Empire," ISBN-13: 9780141927329 0141927321, 2003.