rdtsc instruction access is gated by a permission bit. Sometimes it's allowed from userspace, sometimes it's not. There were issues with it in the past, I forget which off the top of my head.
It's also not as accurate as a the High Precision timer (HPET). I'm not sure which platforms gate/expose which these days but it's a grab bag.
I think you're confusing this and the kernel's blacklisting of the TSC for timekeeping if it is not synchronized across CPUs; but while there's a knob to block userspace's access to the TSC, I am not sure that has been used anywhere except for debugging reasons (e.g. record/replay).
