I have no experience about what the airlines prefer / don't prefer, but the bottom line is there are plenty of guys from both backgrounds in the airlines. More importantly, you have a heck of a long time before that is even a consideration.

In my experience, the guys that show up to flight school with the attitude that they are one day going to be flying with SWA and the military is just a way to get there, usually make complete a$$es out of themselves with the IPs and don't do very well. In the Navy, a lot of 'those guys' are now flying helos (not that there's anything wrong with that) or washed out.

Focus on flight school, do your best, and when the time comes, do what you think will make you happy for the next 8 years of your life. Then you can start to think about the airlines.