If you had to look through a stack of 100 resumes, and 10 were recommended by existing company pilots, would you view those any differently than the rest? Of course you would. Assuming all 100 met the hiring minimums,it would be a safer bet that the 10 being referred would be better applicants.
Why? First off, these 10 applicants most likely know what it would be like to work at that airline-- after all, they know (at least) one of the pilots there. They wouldn't be applying unless they gave some consideration to what the airline offers. Secondly, a reasonable assumption is made that the pilots doing the recommending would not recommend someone they do not like. Have you ever helped a pilot whom you did not care for that much get a job at your company? Probably not.
It is also a numbers and time issue. A pilot recruiter has limited time to go through and select candidates for interview. The resumes or applications that are referred have in effect a virtual Post-it note on them saying "pre-qualified." For a large airline like FedEx which has more than 5,000 applications on file, it saves time to narrow the field down to those candidates already known by the pilot force.
But what about qualifications? Don't they trump all else? In theory-- yes. But in reality-- no. HR departments frequently like to hire a "spectrum" of pilots: military, corporate, commuter, fractional, etc. So actual qualifications (total time, turbine time, amount of college, etc.) vary from pilot to pilot. Once core minimums have been met and some experience is had, the biggest differentiator can arguably be he or she who is the best connected.
It pays to view pilot recommendations as a normal hoop many airlines put up as part of their normal hiring process. Instead of lamenting it, embrace this fact early and begin (or resume) networking like mad. Go to job fairs, visit the big airline pilot forums, jump seat on your future airline of choice, and always have business cards handy. These actions could be the single greatest determinant to your success in landing the job you most desire.