You shouldn't have anything to worry about. Just have the doormen get a taxi for you and hop in. They record the taxi numbers taking their guests.

Alternatively, ask the front desk for a hotel car to take you to the airport, and charge it to your room. More expensive, but if you are genuinely concerned about safety, that will enhance it.

3AM is about the best time of day to be driving around Metro Manila - any other time the traffic is frankly horrific, and your travel times can be measured in hours per mile instead of miles per hour during rush hour on certain routes.