After reading the info here I called back and was again told that AA makes no seats available on the JFK - SFO flights to CP. Just to verify I asked the agent to check another day and lo and behold there was 1 coach seat on a 5pm flight. I then asked her to check a date far in the future and she said she had seats in all classes on all flights. So it looks like I was just misinformed and the agent should have just said the seats were all gone.
I think the main reason I bought off on the first agents response was the fact that I would not expect a capacity control problem on a flight mid-day Wednesday, but after calling AA I was told they had no availability either.
rich