I think atheists would do well to encourage agnosticism, seems like an easier sell to me, training wheels?

For most part they would also do well to eschew evangelism.

I would suggest you read the following two posts:

http://lesswrong.com/lw/ih/absence_of_evidence_is_evidence_of_absence/ http://lesswrong.com/lw/mm/the_fallacy_of_gray/

I think there are several problems with your statements; I'll try to address a few. In the interests of full disclosure, I'm an atheist myself, but I obviously can't speak for anyone other than myself.

Much of the atheist movement reeks of fundamentalism.

I don't know about "much", though some atheists are undeniably fundamentalist -- and some theists are, as well. However, this doesn't tell us anything about whether atheism (or theism) is actually true or not.

By definition atheism is closed minded.

I think this depends on which definition you're using; but something tells me it's different from mine.

So much of science is unknown. I don't discount the idea that the possibility of collective consciousness or any number of other things viewed as supernatural, and therefore dismissed, exist.

Neither do I, and neither do most atheists. In fact, most atheists don't discount the possibility of lots of other things existing, as well: Zeus, unicorns, a teapot in orbit of Saturn, leprechauns, FTL neutrinos, etc. But a possibility is not the same thing as probability; and we humans simply don't have the luxury in believing everything we can think of. We'd never get anywhere if we did that. So, atheists make the conscious choice to live their lives and think their thoughts as though that orbiting teapot did not, in fact, exist. Of course, once someone presents some evidence of its existence, we'd change our minds, and re-evaluate all of our beliefs to include the teapot (or gods, or leprechauns, or what have you).

Read some theoretical physics, we don't understand a lot of stuff.

I suspect we understand more than you think -- there are whole books written on the subject, after all. But more importantly, a lack of understanding doesn't automatically make any alternative hypothesis any more likely. For example, I don't know with certainty how that suspicious puddle under my car got there, but "aliens !" or "demons !" are not the kinds of answers that instantly spring to mind.

That stuff could be the basis completely different ways of thinking about reality.

Sure, it could be. But is it ? If it is, then I'd like to see some evidence. Note that the scientific method has a whole mountain of evidence behind it; your computer, for example, is merely a tiny piece of it.

It's cliche but what if we are programs running on some ultra advanced computer. Would the operator of that computer not be a "god."

I don't know, which god did you have in mind ? And do you have any evidence that we're all programs running on a giant computer, or dreams in the mind of a butterfly, or astral manifestations of Krishna's vibrations, or whatever else one can come up with ?

By definition atheism is closed minded.

Is it, really? I find more open mindedness in "there is no evidence for this, so I have no reason to believe it" than any theism. Someone telling you to be open minded usually means they want you to agree with them: Accepting a solution instead of considering others as well. It's happened to me, when people talked about ghosts, which have been disproven regardless. But then, it's just accepting one seemingly possible solution.

If all unlikely explanations seem possible, how is it open minded to select just one?

Much of the atheist movement reeks of fundamentalism. By definition atheism is closed minded.

A few months have passed since that comment, but maybe you should consider reading: http://lesswrong.com/lw/nz/arguing_by_definition/ and http://lesswrong.com/lw/ny/sneaking_in_connotations/