Flight schools don't issue pilot certificates. The FAA does. The FAA could care less where a pilot recieved training. As long as the pilot meets the standards imposed by the FAA examiner, they get the certificate. The proof is in the pudding.
When people choose schools, they do so for a multitude of reasons. There is no perfect school. The quality of the education and access to resources can make one school more attractive and arguably better than another. I could get my MBA from Montana State or The University of Chicago. The University of Chicago Graduate School of Business is a (if not the) top learning instituions to get a MBA. The tuition cost are indeed higher than Montana State. I bet, on average, that graduates from the University of Chicago are more well rounded and prepared than those from Montana State. A similar argument can be made when it comes to flight training.
I did a lot of research before selecting a flight school. Weeks were spent comparing local schools/instructors with national "big name" schools. It's true I could have spent less money to earn the same certificates, but I wanted a quality, well thought out program that fit my needs. ATP fit my needs.
At the time I was working a 40 hour a week cubicle job, troubleshooting software for a Point of Sale company. I worked 7AM to 4PM Monday thru Friday. Three days a week I would leave work and train at the airport from 5PM till whenever. On Sundays I trained all day. I finished both the private pilot and career pilot programs in 10 months.
ATP had the resources to make sure I had an instructor and required resources (classroom, computers, aircraft etc) each time I drove to the airport. In my 10 months of training there was only 2 occassions where I didn't have access to a plane at the scheduled time. Both were due to other students checkrides going longer than planned.
ATP training is very structured, just like my training at the airline. The checklist used at ATP (which seemed like overkill at the time) are guess what....just as tedious as the checklist I use everyday. The transition was easy.
During my training I met the owner of ATP, just once. He was a great guy. We had a nice conversation during my turn at flying the Cessna Citation. Several months later when I met him again (after being hired to be a CFI) he remembered my name and the details about me and my family. He isn't this rich guy who owns a lot of planes and wants to relax on his yacht while other people run this business. He is deeply involved with day to day operations. He makes sure no expense is spared when it came to safety, mantanence or training.
I did take the ATP Regional Jet Course and went on (after being hired by my airline) to go instruct the course. Guess what? The training in that course is just like training at the airline.
While training at ATP does cost more than similar training at a local/smaller flight school, the training, equipment, and access to resources make up for it. In my opinion at least. I've seen people price out the same training offered at ATP and come out $3,000-$7,000 cheaper. That's a lot of money no doubt. But there is truth to the old saying, "you get what you pay for". Just visit a few pilot forums to see the stories from people who got ripped off by flight school X, or were overcharged (by dragging out the training) by flight instructor Y, or having trouble learning because the flight school keeps changing aircraft (going from a Piper to a Cessna to a Diamond isn't good when you're just starting out). It happens.
In full disclosure I am not and have not been paid/compensated by ATP for anything I have written on this blog. I'm just discussing my own opinion and experience while going there.
With that said, ATP recently posted a new video/commercial.