Although in this case, I would speculate that maybe Roddenberry or Herb Solow decided that "S.S. Yorktown" was too specific to American history, and Enterprise would be more universal. Although I'm not sure that's a good speculation, since they never seemed to have a problem with an American bias otherwise.
Perhaps it was that Enterprise is a name with a more extensive historical pedigree, with more ships bearing the name. Perhaps it was chosen because the USS Enterprise CVN-65, commissioned in 1961, was the first nuclear-powered aircraft carrier, so they thought it was fittingly futuristic/pioneering.
In one of the documentaries (I don't remember which one), Roddenberry said he changed it because "I thought Enterprise
was a better word". That's a direct quote.
I have to agree. It does roll off the tounge better than Yorktown
Weither this is true or not, I don't know, but I heard it from Gene's own mouth.