What if the virus that everyone is infected with is actually a virus that causes disassociative visions, hallucinations and anti-social behavior? Maybe Rick is seeing "zombies" because of his virus, but really he's on a rampage through the real world killing people. He wakes up in a hospital. Then he goes (eventually) to the CDC. Then he ends up in prison. I think this is a journey lots of people with uncontrolled psychotic breakdowns go on.
We know Rick isn't all there mentally. I mean, his phone isn't connecting to the switchboard, that's for sure. This would explain all those moments that don't make much sense in the show, because we can say, "That's all part of Rick's hallucinations."
Poor guy. And here we are, watching the guy's psychotic episodes for three seasons.