I am a D.O. and matched into an allopathic cardiology fellowship program (2nd tier program nationally, U.S. large university-based). I did my residency at this same institution where I currently serve as Chief Resident. Ultimately, a good resident makes a good cardiology fellow, however you will find considerable bias coming from an osteopathic residency applying to an allopathic fellowship program. Why? For one, the majority of fellowship programs (the majority) are in large, university based settings. The faculty there scarcely know allopathic community programs much less any osteopathic programs (be they community or the few true university-based ones in existence). Secondly, I recall from my interview trail around the country that many of my interviewers knew my letter writers, who happened to be prominent nationally and even internationally in the discipline. Very often, interviews are granted because of who knows whom. This puts osteopathic residency applicants at a severe disadvantage, at lease when it comes to sending out large numbers of applications to the most common type of program out there, the large university based program.
As far as DO fellowship programs, I'm not familiar with who they take (e.g. from within their own ranks or not).
Here are some statistics which might further clarify the nature of allopathic cardiology programs and who they take: in last year's NRMP Cardiovascular Medicine match, there were just >700 fellowship positions in the match. The number of DO's matching? exactly 25.
Coming from an osteopathic residency program, your best bet would be to set up electives at programs which have historically taken DO's in their fellowship program. You can explore the websites of these fellowships to see if there are current DO fellows in the program. This is probably your best bet, however having said that, I did just that when it came time to apply to programs, and ironically I was not granted interviews from so-called "DO-friendly" programs. At any rate, it will require a lot of self-motivation and self-endorsement but I would not say it's impossible...