From the college's point of view there are three basic departments at work, each with their own responsibility(s). These departments are Admissions, The Deans of the School within the college you’re applying to, and the Department of Athletics. And as Steven just pointed out, the demand for the schools at the very top of name recognition, prominence, and so on - have the toughest entrance criteria's going. Not that their impossible to get in to - just challenging to say the least.
Ok, enough of the generalities - lest get down to the floorboard stuff.
Admissions responsibility along with the Dean from each School within the college's structure has a minimum standard that they will accept and much below that standard flows under their bridge. So, let’s say you’re applying to Boston College and you'd like to be an attorney. Well, the college's School of Law pipes in and says that's all fine and good but here's what's required on your part. The Admissions office along with the Dean of Students of Boston College's School of Law look over your application, GPA, certain accepted pre-college tests, and it's either a go or no go.
You can have the best arm the scouting world has every seen, but that won't cut it if the stuff that you bring to the academic side of the equation fails. So, like Steven said, matching your academics to the college standards not only helps you, it also takes a big load off of the Director of Athletics and the Baseball Office and it's coaching staff who does the recruiting.
By the way, a good place to start - if you haven't already, is to look into the NCAA Clearing House and that part of your process. The earlier the better. Also, start reviewing your CORE requirement for the colleges and universities that you might be interested in and any major that sets the ground rules for those CORE requirements. For example, look at the CORE course requirements for a premed curriculum verses a philosophy curriculum.
Best wishes with your college career.