Medical schools charge for applications for a simple reason: to discourage applications from people who have no chance at those medical schools. If they didn't it is a strong likelihood that many more aplicants would clog the system, creating ever more work and delaying everything and everybody. Admission offices are expected by the medical schools to partially pay their own way. If applicants create work, even if they will not even be seriously looked at, then the applicant will still have to contribute to the cost.
Applicants have to be selective where they apply. Having high grades and high MCATs does not mean the welcome mat will be out everywhere. Omitting the public medical schools where state residency is often an important factor, even the private medical schools have preferences for where their medical students will come from. Some of it has to do with their estimate of what grades means at different colleges, part of it has to do with letters of recommendation and their trustworthiness; letters coming from committees and advisors whom they know and trust usually carry more weight than lettters from faculty who are unknown to them.
Think about it. If you were running a business, say, and had to decide on whom of several job seekers to hire, if you wanted letters of recommendation wouldn't you give more weight to those from people, who, from past experience, you know and trust to be honest?
You should always try to imagine yourself on the other side of the desk. What would you do in the same circumstances, if the shoe was on the other foot, so to speak? Treat all grades as equal in meaning, no matter the circumstances and where earned, treat all letters as equally believeable no matter who the writer?
All of you know students with high grades you would not trust to shine your shoes, let alone be your physician. All applicants are equal, but some are more equal than others.
