Question about honda certified used car warranty

I purchased my Honda 1998 Accord LX from my local Honda dealer June 7,2002. I was told that I would have full coverage for one year; then drivetrain warranty until 100,000 miles or 2005. I took the car in to have a noise looked into [whine]. They charged me $39.95 for "diagnosis"! They supposedly drove the car for 2.5miles[according to odometer] and ascertained that the sound I heard was NORMAL. I just wanted peace of mind and to have this complaint recorded. Was I ripped-off or is this the normal policy? Thanks very much for any information you can provide.