Generally, it's better to have a GFCI than to not have one. However, they don't protect against everything, so the presence of one is no excuse to get sloppy about safety.
In particular, as Kizzap says, they only protect against faults to earth.
As a consequence, if you're using mains to feed an isolating transformer, a GFCI offers no protection whatsoever to anything on the secondary side of the transformer. The GFCI merely insures that the line current going to the primary of the transformer is all returned via the neutral, but the GFCI doesn't "see" anything that's happening to isolated secondary.
This sort of situation sometimes comes up on a test bench when someone uses a 1:1 isolation transformer in order to "float" a device under test so that a non-isolated oscilloscope may be used to probe it. If you clip the scope's ground lead onto something that is close to line potential on the DUT, then other parts of the DUT normally at neutral potential may carry full mains voltage with respect to ground. Touching such parts of the DUT while touching something grounded could give you a solid shock of mains voltage, and the GFCI won't prevent it.
Of course, without a GFCI, you'd still have the same potentially dangerous situation when using an isolation transformer. The GFCI didn't make anything worse, unless it made you feel invincible and protected, causing you to drop your guard.