Do you tune all your percussion to your root note or is it just the kick drum? Are there any exceptions?
Not necessarily the root note - that would be boring - but something that works harmonically, yes. I always spend ten minutes tuning my bongos before I play them, just like you would a guitar.
Kick and bass are different because complex harmonies don't tend to work so well in the lower octaves.
An interval of a fifth can work well though. If your bassline is in E minor a kick tuned to a low B can be very effective.
Or it may just sound shit. You never know until you try it.