The RMS is fairly heavy (905 pounds according to this source), so it's only carried when necessary. It wasn't needed on this mission, so it was left on the ground. It would've been so much dead weight.

I'll have to check some numbers, but it's possible Columbia would've had trouble carrying SpaceHab and the RMS at the same time due to weight limits. It may be more likely that the RMS would've been difficult to operate with the SpaceHab in the cargo bay. Complicating factors might include reduced visibility for the operator and perhaps mounting issues when the SpaceHab is installed.

Instead of mandating carrying the RMS on every mission, something along the lines of the AERcam might be a better idea.