I would say that the main themes are cold-war era political fears as well as global ecology fears (global warming, pollution, etc...) It's pretty easy to see this as anti-communism, and anti-pollution, but I think Neil was really trying to engage the idea that it was more about an invasion instead of a devastation. About something evil coming in, or I should say, creeping in like the tide. But I don't think it was specifically aimed at the Soviets or the environment as much as it was a general Libertarian fear of a dominating force. It's almost more 1984 (book) in it's understated elements. Or maybe even a throw-back to Nazi Germany. (I like to think of it as a prequel to Red Sector A.)

Nature has some new plague To run in our streets History some new wrinkle We are doomed to repeat

Here Neil is saying that it's happened before, but not in the same way. I think Neil was expressing the fear of a totalitarian government taking over and putting it in terms of a global extinction event. Saying that it could just so easily sweep in like a hurricane, or asteroid impact. That when it does happen, it would be devastating, unstoppable, but that if we act now, we could potentially avert it.

The title itself, Red Tide, seems to have a trifecta of meaning. Literally red tide, a toxic bloom of red algae than can destroy an ecosystem. Also potentially meaning blood, i.e. massive bloodshed. And finally, the idea of an invasion of Communism (reds). I think to Neil, it might as well be one and the same. I think he saw the effects of Communism as bad as a global extinction event. And that it would be nearly unstoppable if it got a foothold.

Chalk this one up to Neil reading a lot of Ayn Rand.