...My question is how do you, as a parent, come to terms with the fact that your son is that good? It might sound like a strange question, but I have always taught my son and lived my life of trying to be humble (not always successful). But now he's showing me that he's got a special talent. I don't know why this is difficult for me to grasp, but I'm having some anxiety over this. I've come to think it might be the fact that, if he plays college, he'll be gone (he's my oldest child) and I'm having a small issue with this. ...
A big +1 to what bballman said...
All of our kids have special talents of one sort or another. Some will get more outside attention associated with theirs. What is most important is to always keep in mind what is most important. Outside of baseball (or any other special talents), what are the most important things you want to instill in your kids? You mentioned being humble. That is a great one, IMO. Never waver. Don't allow the attention from his talent blur your parenting vision. Be sure you are consistent with your message. Great game, questionable behavior? Address the behavior. Bad game, handled admirably? Praise the character.
At some point, baseball will not be the center of his life. What character traits will you have taught him along the way?
As far as help with anxiety over the young man leaving, they will all leave at some point. He will be the easiest one because you will still be fully engaged in parenting the others. Wait 'til the last one leaves 
. Continue enjoying the ride.