In Auto or one of the easy program modes (portrait, macro and night (???)) the flash should pop up automatically in low light situations. (Page 70) In Program, Aperture Priority, Shutter Priority or Manual, the photographer has to depress the flash release button (lighting bolt) on the left side of the viewfinder housing.
To rotate through the modes, you need to depress the flash release button and turn the main command dial (rear dial) at the same time. That should scroll through the flash options.
Now then: the D90 might have a custom function that switches the front (sub-command) and rear (main command dials), so you might want to check if the FRONT dial changes any settings. I do NOT believe performing a two-button reset will reset this change.
Okay, I just downloaded the User Manual: Menu F/f5 Customize command dials. (Page 201) Electronic copy of the English D90 user manual can be found here.