I'm not sure the chances can be compared, since the likelihood of medical school depends on local factors, such as your ROTC battalion, your CO's evaluation and senior NCO's observations, and yearly variation based on capacity - as well as the normal factors like GPA, pre-requisites, and being accepted to med school first, before you actually apply for that service selection.
However, med school out of USNA is usually restricted to a very, very few new ensigns. For the class of '15, it was 12. Those 12 have no doubt been preparing since plebe year. They've arranged to take courses like introductory biology, microbiology, cell biology, biochemistry, and genetics - medical school pre-requisites, many of which are not available at USNA - at other universities, in addition to their heavy load of academics, military, sports, and ECs at USNA. In addition to their required summer training, they've arranged for internships and co-ops and to shadow physicians, nurses, PAs, PTs - again, that the vast majority of successful medical school applicants also do. They take the MCAT and go on medical school interviews. Only when they are accepted to a medical school can they request restricted-line duty, and going restricted line is another bureaucratic path they must negotiate. I'm not saying it can't be done, since clearly 12 mids did it last year, and a similar number the year before, and the year before that, and so on. But this is a really hard path to medical school and it's not at all guaranteed.
No one can really compare coursework at USNA to other colleges and universities. Here again, there's so much variation at a small scale, such as among all the different course sections of plebe chemistry at USNA and regular freshman chemistry at a good U.S. university. In fact there's probably more variation within an institution than between, say, USNA and the University of Michigan. However, I've taught at several colleges and two universities, and based on comparing the syllabi (course plans that students get) between USNA and other top colleges and universities, USNA's courses are just as demanding, just as rigorous, require just as much work and self-motivation as other reputable colleges and universities. A 3.8 GPA, never mind the overall order of merit, is a rare (but still attainable) accomplishment coming out of USNA.
If you are asking because you're strongly considering medical school after you earn your Bachelor's degree, my sense is that you'd have greater flexibility and better chances out of ROTC.
One other option you might investigate is USUHS. You can go through regular civilian college, earn a Bachelor's degree, meet all the necessary requirements and pre-requisites, and enter into medical school at USUHS. You are directly commissioned as an O-1, you receive free tuition and the salary and benefits of an O-1, and your service obligation is 7 years after you complete your residency. As you can imagine, USUHS is pretty competitive too.
