Along with some of the other deeper problems listed in other replies, here are some others:
Poor driving skills and habits. California drivers are specifically taught not to zipper merge and will get angry if you do. Plus, they weave looking for the fastest lane. This weaving means others don't leave following distance (else some ****** will take it), so there is no cushion and everyone stop/starts.
Poor interchange spacing, requiring excessive merging. This is especially true in California, where there are no standards for interchange spacing. Poor merging skill makes this worse.
No functional hierarchy of roads. California has 26 lane freeways or 2 lane city streets, but few arterial and collector roads. This goes hand in hand with poor interchange spacing, because you need lots of interchanges to the city streets, rather than a few interchanges to arterials.
Poor interchange and intersection design. California loves four leaf clover interchanges because they reduce left turn conflicts on city streets, but they often back up the freeway instead. Also, cramped interchanges result in creative interchange designs, which often have capacity problems, backing up onto freeways.
Poor traffic light timing. Often lights rely on triggers, and very few lights are synchronized. Even if they were synced, poor driving habits mean that people speed between the lights and are forced to stop.
HOV lanes often make these problems worse because people merge quickly to get into the HOV lane and then to get out. Theoretically they increase capacity, but only under a very simplistic model, and not when you reward electric vehicle owners...
Hopefully self driving cars will help with some of these, if they can be taught to drive properly, and co-ordinate merging, but then mostly their owner will get frustrated because they will always feel they could drive better.
The root cause of these problems is that a fundamental theorem in traffic basic shows that at optimal traffic flow at any point is defined by the condition that every individual driver can improve their own solution by acting selfishly. With selfishness on the rise, it is no wonder that traffic problems are getting worse.