At the present time, I cannot find a statement by Roddenberry concerning the change from Yorktown to Enterprise, nor from TOS personnel such as Matt Jefferies.
In lieu of a statement, I will offer speculations.
Historical and technological significance
When Roddenberry pitched the show in 1964, the actual USS Yorktown (CV-5) would have been remembered for being sunk by the Japanese during the Battle of Midway, only 22 years earlier.
The USS Enterprise (CV-6) survived not only the battle but the war as the most decorated US ship.
Not only has the Enterprise name been given to a healthy line of decorated ships, it also would have represented the cutting edge: the CVN-65 Enterprise, built in the early 1960s, was the world's first nuclear-powered aircraft carrier. This powerful symbol of progress and achievement may have had an impact on the naming of everyone's favourite starship a few years later.
At a practical level, "Enterprise" sounds more universal and less US-centric than "Yorktown", and hence fits with Roddenberry's pan-humanist beliefs.
It sounds sexier. Note that in Roddenberry's series pitch, Robert April was the captain. Enterprise + Kirk is decidedly sexier than Yorktown + April.