I suppose, It's about the environment. There are many factors to consider.
First, logistically speaking, transport, supply and communication lines in the Philippines are hard to establish because we're an archipelago of 7,000+ islands. The unique geography makes it hard for mass evacuations. Go to high areas, suffer landslides and wind damage, stay low, storm surges wipe you out.
I don't know much about the Indian typhoon season, but the Pacific typhoon season, since the 90's on average, starts at January-March and ends at November-December: it doesn't stop. Fortunately we've had good years, such as the 1998 storm season, the first storm system formed started in July at that time. On average, most of the Pacific storm systems hit us every 3 weeks, there are certain months where parts of the country get hit by a typhoon every other week. So almost all resources are poured into constantly getting supply lines and shelters re-established.
Given this, we Filipinos have been taught, even the children, to consider typhoons to be normal and to have their distinct personalities to look out for. I remember back in 2009 that we took a direct hit with Typhoon Ketsana (Ondoy). It wasn't expected to deal that much damage since Hurricane strength is generally associated with wind speed, the measured wind speed wasn't that high. What we didn't we know was that it brought 454.9 mm rainfall in the Metropolis, flooding rural areas in our capital region as high as 4-6meters. Uncertainty is high, resources are low, the islands of Samar and Leyte got hit badly: the eyewall brought in the surge from the east and when the storm passed by, the tail surged the sea inward from the west.
Also, it's hard to get good data. Info and news from the media and government are unorganized, each have their own databases, and not to mention, their own agendas to look good.
Majority of Filipinos consider the lack of financial resources as the biggest factor due to politics and corruption. As mentioned in the comments above, the mayor of the city of Dumaguete can only set aside something like $9,000 USD. Not a lot of resources, considering that's just enough to buy a car here in the Philippines.
The lack of resources and wealth, the difficulty of re-establishing supply lines sets up an environment for such casualties despite preparations.