The biggest difference that you will notice is that in the MLB players can only use wooden bats. If a MLB player used a metal bat like they do in the NCAA there would be a lot more home runs and they would go a lot farther too. On top of that, with the speed that pitchers are now throwing at (the league average was around 92 MPH) it would increase the danger factor exponentially. If a pitcher got hit in the head with a line drive off a metal bat, chances are good he would not survive.
I don't know how familiar you are with Minor League Baseball but generally speaking when a college player gets signed to an MLB team they will be sent to their Single-A affiliate unless they are insanely talented. When that happens it is for most of the players the first time that they have had to use wooden bats all the time. For that reason Single-A is considered an 'instructional' league so that players can get used to the bat.
There are a whole bunch of other differences but that is the biggest one.