No, they're not scared of DOs. I do think some parts of the larger medical community are upset about the fact that 28% of the future ACGME board will be inhabited with representatives of the AOA/AACOM. This entire discrimination thing is sort of a nonissue, because it'll slowly be worked out once the merger is completed. Having 1/4 of all the votes is a tremendous amount of power for a small minority of physicians. Eventually, someone will want a pet project/policy approved and the DOs, who are linked by a common heritage, degree, and shared experience, will cash in their ticket. What price do you think the DOs on that board will exact on anyone who screws with their students/residents?
But none of that will happen. Why? Because the vast majority of ACGME PDs will be interested in finding the best applicants, regardless of where they came from. Will that always be a DO? Of course not. Remember, we're a minority. You're never going to see a DO in every residency class. That's unrealistic, but you will see programs slowly open their doors to the possibility. How do we know this? Because so many programs already take DOs. Sure, there will be doors closed for years to come, maybe even forever, BUT eventually the number of places with the nuts to flat out advertise they don't rank DOs will dwindle. They'll just have to get by softly discriminating based on perceived prestige or whatever.
Osteopathic medicine is 65,000 people who are almost all represented by a cohesive, albeit sometimes contentious, lobbying body. That number grows every year. The AOA has been doing the above for over 100 years. They're like your eccentric uncle who sometimes talks about the recent trekkie convention. Lastly, I would encourage every DO student to remember one thing: you don't want to match somewhere that doesn't appreciate you. Don't worry about it. Any program that turns away an excellent applicant, both on paper and after observation, just because they went to a school they don't like is not a program you want to be a part of. When you're in school, do your best, take your boards seriously, and get out there and impress on rotations.