Why are my teeth throbbing after a root canal?

In the area of tooth pain, and pain after root canal treatment, an endodontist (root canal specialist) is the dentist you should continue to see.  However, if your endodontist isn't able to diagnose your problem then you might be best served to "get a second opinion" from a different endodontist.
Regarding why still having pain?  Could be a number of reasons.  The tooth could have a small fracture in it.  It's possible there was an extra root or nerve in the tooth that wasn't detected or unable to be filled.  You could have a residual infection that doesn't show up in the x-ray.  Your bite could be "high" (meaning, you may be hitting harder on that tooth than the rest and need your bite adjusted).  You might have sinus problems, and sinus problems often mimic tooth pain on upper teeth.  You could have periodontal disease or a gum abscess down the side of one of the roots.  You may have a neurological condition called "trigeminal neuralgia".  You might also have "referred pain" from another tooth. 
So, since there are so many possibilities, I doubt that any dentist will be able to answer your question without a thorough evaluation.  Thus, again, I refer you to an endodontist. If you're not getting the answers you need from your current one, then see a different one!
He may send you for another opinion from a neurologist or periodontist if he can't find any pain he can attribute to the root canal or nerve that was once in the tooth.