The Catholic Church and many organised religions in the Philippines continue to be very powerful, influential, and profitable institutions. And it is in their interests to maintain the status quo and the dismal state of enlightenment of the source of their power -- the average Filipino.
Because many Filipinos continue to be beholden to Church dogma, politicians who, as in most democracies, are elected by popular vote, will continue to pander to and, worse, defer to the influence of the Catholic Church. It is an interlocked matrix of tradition that Filipinos are imprisoned within.
I'm not an expert in world history but if I recall right, enlightenment and a re-surgence of critical discourse that started in ancient Greece (which was lost to the Arabs during the Dark Ages) somehow began to bubble up from the grassroots in Europe sometime in the 15th Century. Still it took centuries before the scientific method triumphed over religious primitivism in European governance.
Again, considering the unprecedented access to knowledge and technology enjoyed by a broad swath of Philippine society, religious mumbo-jumbo continues to lace much of Filipino thinking and conversation. I have no problem with religious faith. But I firmly believe that religious orientation and spirituality are personal things that should be left out of matters of state. Furthermore, I take issue with people who presume to be "blessed" by their god which begs the question (as you also pointed out) of why other people may not be as blessed, such as the thousands that died in the latest "natural" disaster to hit Mindanao. I elaborate on that sentiment of mine in this article.
Indeed, much of the reason behind why change is slow in the Philippines despite the existence of obvious solutions to many of its problems can be traced to the influence of organised religion.
[NB: This article was originally published as a comment on Get Real Post.]