I have a 2004 RX 330 with NAV. It will be 1 year old in August. When I ordered the vehicle, the dealer gave me an instructional DVD that really helped to familiarize me with the basic NAV functions. When I took delivery he spent some time with me to review the NAV system operation. I never had problem using it and it now seems very intuitive.
I know now that I would never buy another car without a NAV. It has saved me much time and fuel and makes long trips much more relaxing.
I'd be curious to hear about the problems you're experiencing.
Best Regards,
JGT