Why were native Filipinos subjected to less cruelty by the Spanish colonizers, as compared to natives in the Americas?

I can't give a comprehensive answer, but I have been searching some sources that may give some clues.

When Spain arrived at Philippines, it found an existing administration structure, the Barangay, which "coupled perfectly with the spanish municipal regime". These structures were isolated from each other and didn't form a state or any kind of centralized government that could oppose the spanish rule, and were absorbed, not destroyed. "This social disintegration immensely facilitated the conquest; and by tact and conciliation, effectively supported by arms, but with very little actual bloodshed, Spanish sovereignty was superimposed upon these relatively detached groups, whose essential features were preserved as a part of the colonial administrative machinery". As proof of the relatively peaceful coexistence, in 1590 the spanish army present in Philippines had just about 400 men, and it hadn't increased significantly by 1786 (source in spanish)
In Philippines, religious orders had a stronger influence. The christianization process was fast, natives respected priests and that granted them a stronger de-facto authority, the spanish authority needed in practice their tacit approval. Priests refused to allow encomenderos the kind of abuses that had been present in America. As proof of the impediment that priest represented for the local authorities, they often complained directly to the monarchy about the obstacle that in their opinion priests represented for the advancement of the colony. Priests defended their power using their influence in natives or even religious pressure such as denying sin's absolution to local authorities (source in spanish)
Spain arrived at Philippines when the colonization methods used in America had been "refined" and stabilized. The colonization process was regulated by law, Philippines colonizers had to comply with newer colonization regulations. Priests had already successfully managed to get included some kind of "rights" for american natives in these laws. Unlike what happened in America, where the protectionist regulations were largely ignored by encomenderos, priests in Philippines made sure the laws were enforced, even when non religious spaniards complained that it was almost impossible to comply with them.
The main source of wealth of spanish colonizers was trade with asia and mexico, so exploitation of natives didn't become a critical economic issue.
As mentioned elsewhere in the thread, natives were less vulnerable to european diseases (I have read two explanations for this while searching info for this thread: previous contact with diseases from other asian countries, and the fact that spanish colonials always were few people)

Along with lack of epidemic diseases I'd guess because the main goal of the Spaniards in the Philippines was the galleon trade as opposed to resource extraction. In the Americas they focused on mining or large scale agriculture fueled by native labor in conditions approaching slavery whereas in the Philippines the main commercial activity was trade with China and to much a smaller extent agriculture, as well there was much less demand for cheap native labor in agriculture because of the large amount of Chinese immigrants.

http://web.stanford.edu/group/journal/cgi-bin/wordpress/wp-content/uploads/2012/09/Merchant_SocSci_2009.pdf covers some of the economics of it and http://historicaltextarchive.com/sections.php?action=read&artid=295 on the American economy