SNL makes fun of everyone, that's what they do. Yes this skit is making fun of government employees but other skits make fun of celebrities, other skits make fun of bank CFO's, etc. We can't take it personally if they choose to make one skit about Gov't employees.
On the bright side, I do think this stereo type is disappearing. I live in Washington State and the DMV (we call it DOL) has improved ten-fold since I moved to the state. They've automated many services and you can even go online to check the local wait time to see if it's worth going to that day. I'm not a DOL employee and I've had more than one bad experience there, but I can say that in the recent past, I've noticed drastic improvements. I say we take this skit and use it as motivation to find even more efficiencies.