Kaepernick said he felt it would be hypocritical for him to vote because it would be the equivalent of showing support for a system he doesn't believe in. He also said the choice of Trump should increase the urgency for everyone to work toward solutions to make the system better.
I don't think he should be criticized for that I think his logic is sound. If his reason for not voting is because he believes the process is broken and corrupt, then he's right. He also said there are other ways to create change which is absolutely right. Now, whether or not what he's doing personally is creating change that's up for debate but he had created a whole lot of conversation that's for certain.
I agree with you though, on a local level you can accomplish a lot more and I'm not sure if that's something he considered or if he was just focused on the presidential election. I don't know his motives other than what he stated but throughout history there are plenty of examples of voter boycotts.
One example that immediately comes to mind is The Bolsheviks advocated an active boycott of the Duma. Lenin called the Duma, introduced into the Russian Empire by Tsar Nicholas II in 1906, a "fraud that must be exposed". Boycott meaning refusing to take part in the elections. "Why do we refuse to take part in the elections?
Because by taking part in the elections we should involuntarily foster belief in the Duma among the people and thereby weaken the effectiveness of our struggle against this travesty of popular representation." And he goes on to list more reasons here -
Lenin: Should We Boycott the State Duma?