No one is saying military pilots are better than regional pilots. If you look at it from a purely experience standpoint, then yes regional pilots that have been flying in and out of the same hubs for years would be the obvious choice. However the major airlines are looking for more than just the experience.
What the military pilots posses that is missing from most regional pilots is what I would call the "mission mindset" Military pilots, especially recently separated military pilots, approach the job of flying the airplane as a mission. They feel it is their duty to get the airplane from point A to point B no matter what.
Regional pilots on the other hand feel it is there job to get the airplane from point A to point B in the safest and most efficient manner within the confines of FAR 117 and the contract.
Military pilots are used to following orders and are more likely to waive provisions of the contract to help the company (thus completing the mission) than a regional pilot that has been getting screwed for 6-15 years. Military pilots are less familiar with working under a union and a contract and less comfortable with telling people no.
I was former enlisted military and it takes time to change from thinking "this is a mission that must be accomplished" to realizing "this is a job that I will do my best at, within the confines of the contract"
If legacy carriers were really concerned with knowledge and experience then the interview would still consist of ATP test and simulators, instead it consist of hogan test, personality assessments, and HR meetings.
They assume we are all nearly equal in terms or trainability, mold ability, and adaptability. They are looking for the individuals that will work hardest to ensure the companies mission success. Since military pilots in general already conform to a certain mold, it is far easier for the legacies to draw from that pool than it is to screen thousands of regional pilots.