That's why I say it would behoove you to do your research. Try to learn as much as you can about the program, find out about current research projects the faculty is presently investigating, try to get to know those faculty whose projects you are interested in, etc.
I couldn't disagree with your post more. The top programs are top ranked for a reason. The rankings probably mean more for MD/PhD students, since they take into account NIH funding levels, than they do for MD students. It's no coiincedence that if you look at the rankings and compare it to a MSTP list, all of the MSTP schools are top in the research rankings consecutively from 1 on down into the 30s if I recall correctly. There's extremely few outliers--almost no MSTPs outside of the top 30s and I think every school in the top 20 research rankings is MSTP now (Mayo was the exception up until a few years ago). Then when you go better in the rankings, the larger programs tend to be more and more highly ranked. WashU and Penn are #1 and #2 in size. See where they are on the rankings?
If you even try to research programs, it's impossible to know what you're looking at until you go to a program, and even when you interview you get a very skewed and selected look at a school. Websites are often times out of date, cheerleading, and misleading. Labs you look up on websites sometimes no longer exist, are going to move, or won't take MD/PhD students for a variety of reasons. If you've never been to a location, you wouldn't know how nice or not nice it really is until you go and look for yourself. When I would list faculty I would like to meet when I would interview, I almost never got them. The real reason was sometimes because they were unavailable, but more often because they were mostly clinicians who had some interests but no grad students or they had no funding or they were awful mentors, etc etc etc... The MD/PhD offices of course screen these lists but don't tell you and you won't know about these things until you're a student at a program locked in, and trying to find a lab. So again, larger schools with more and more options, especially in your area of interest but not necessarily, are KEY in where to apply. The rankings reflect this size and number of options. It doesn't necessarily reflect location, which I think should also come highly into consideration. Then again, you wouldn't necessarily know (I didn't) that Northwestern is in a beautiful area of Chicago and UChicago is a really ugly part of Chicago until you go to interview.
The absolute worst advice I got when applying was always from my undergrad advisors and faculty. In retrospect, they had no clue where to tell me to go as a MD/PhD, but always sounded like they were sure of themselves. I wish I had applied to more of the schools in the top-20, because honestly I applied to a lot of schools that were totally wrong for me based off of being told "Oh, they're strong for X" when in reality the lab that made them strong in X moved 5 years ago or people telling me how nice Cleveland was to live in, for example.
There was also this sense from SDN that I didn't want to be a numbers *****. I should have some genuine interest in the school rather than just numbers. Yeah right. Whatever interests I had at the time were mostly misplaced and kind of irrelevant because again, I was a premed and had no idea what I was doing. I ended up doing something completely unrelated to what I started doing, and I'm so glad I went to a big name school because we're strong in many, many things and I had those options to choose a lab in what became my clinical area of interest. As a result I couldn't be happier with my lab, but it's almost only the big name schools that are strong in this area of medicine. I would have not had nearly as many options at my second choice program (ranked in the 20s) and I would have been sent to a campus an hour away for what I do. So in my mind, ranking, either MD or grad school, is one of the better reasons for choosing to apply to a school. It shows a strong reputation and high number of faculty generally or in your area of research.
I know it's an unpopular opinion to say "Go off of the rankings", so I fully expect to get flamed. That's fine. I just wanted to put my opposing viewpoint out there.
And since the plural of "anecdote" is "fact," clearly we have our fact straight. 
