Philippine Airlines is pretty reliable when it comes to domestic flights in the Philippines, in-fact, I think they offer the best service and product in the Philippines. However, they don't fly from MNL to Caticlan (the closest airport to Boracay) but their sister company Airphil Express does. PAL does fly to Kalibo, another gateway to Boracay, but it's around 2 hours from Jetty Port (where you take a small boat to Boracay Island) I recommend you flying to Caticlan Airport since it's only 5 minutes away from the port.
If you're going from MNL to MPH (Caticlan) I highly recommend Cebu Pacific. 5J operates the ATR-72-500, which IMO is better than Airphil's Dash-8. I've been on both airlines and 5J is better when it comes to prop planes.
All flights to Caticlan are operated by prop planes, if you're uncomfortable with that, then go to Kalibo instead. PR and 5J operate A319/A320 to Kalibo. So, if you choose to go to Caticlan, pick 5J. If you choose to go to Kalibo, pick PR.
As for safety concerns, PR and 5J operates the A319/A320 domestically (A330/A343/747 on major domestic routes), most of them are relatively new, so you don't have to worry about anything.
It's a cultural thing.