They're good fun, and can be useful for some things - e.g. when I was doing my stall training I really messed it up first time (incipient spin, yukk) so I went home and nailed the procedure on FS for about a week...following weekend my stall recoverys were perfect
However it does lead to both a false sense of security - it really does make a Boeing 737 seem so easy! - and laziness in my case - autopilot on, let the a/c fly itself etc...
However, as has already been said here, more than one instructor has commented on how useful the navaids are & how you can set it up for approaches, holding points & other IFR scenarios.