Since footballs do not instantaneously transfer from the hand of the QB to the intended target, passing windows are a factor of both space and time (i.e.: the football must travel through a physical space, and must do so within a certain time in order to arrive within the "window"). Assuming that the airspeed of a rookie QB's thrown football does not vary significantly from their football airspeed during the last year of college, the increased footspeed of everyone on the field (i.e: "game speed") means that passing windows are necessarily smaller. The windows have to be smaller, even if the physical dimensions of the passing window are the same, because the ball will travel at the same speed but must do so within a narrower envelope of time. 

Additionaly, NFL players are much more experienced. NFL defenders are able to react more quickly and instinctively than college defenders - eliminating one of the advantages that college football offenses enjoy. 

Finally, NFL defensive schemes are more sophisticated and are able to defend more points along more route combinations than college defensive schemes. This often requires both QBs and WRs to make reads throughout the progress of a play - with correct reads leading to a WR selecting the correct "option" along their route and coming open for a split second before the defense can react. These option routes lead to small and quickly-closing windows (windows that often must be anticipated and thrown to before they visually become "open") which are simply not typical of the college passing game.

NFL passing windows are significantly smaller than those seen by QBs in the NCAA.