It seems that the phrase "Our Futures one big Zero" refers to the thought that there is no afterlife (future), that all we have is now.

Materialist is not, curiously enough, about materialism. Notice how he actually pronounces materialist. He says "mata-realist", stating that he is basically a realist in that he sees this is a materialistic world. But more than just materialism, he sees basically the little chance that our world has left, and because he recognizes this, he is a realist. Materialist is just a clever way to state that he is a realist, the song isn't totally focused on the quest for material objects.

Line 1-3: I think these lines are a way of saying that by the time you realize that you should be living your one and only life, you will be too old and feeble to be listened to.
Line 4: I think this line means that life isn't just a short break from some greater plan and that these 50-100 years are the real deal and all we have.
Line 5-7: He is basically talking to what he sees as a fake God and saying that he'd like to believe that there is something beyond life. But the evidence is against it so you just have to clench your teeth and live your own life.
Line 8-9: A materialist is someone who is only concerned with the life he/she is currently living. A realist is someone who doesn't beat around the bush and takes things for what they are. The ideas go hand in hand.
Line 10-11: Basically translates to "It's too hard to swallow so I'll just resist?"
Line 12-13: A materialist, only thinking of the present and his/her life, would not be afraid of some final judgment in the end.
Line 14-15: The facts (or lack there of) are in plain view so a materialist would not want to be told there is something that may or may not be unveiled at the end of his/her life.
Line 16-17: There is no point to seeking a higher ground mentally if it allows the physical world of the present to get to you.
Line 18-20: Basically, life sucks then you die. Is that part of a master plan?
Line 21-23: Sometimes it can be helpful to belief in something like God or grand design but it's only for those who have no faith in the world (this also applies to line 24-26).
Line 27-29: A deist is someone who believes God created the universe then abandoned it. The singer is saying that he's not trying to move on from some terrible abandonment, but the he just does't care about anything other than his worldly possessions.
Line 30-33: Nero was the ruler who caused the massive fire in the Rome. He's saying that after this, nothing's waiting for us. The second line (I think) means that we should forget the past and make due with what life we have now. The third and forth lines in this group mean (I think?) that even after all we've been through we still try to appease some God by putting ourselves through physical suffering (such as climbing a mountain) and the spiritual strain of trying to make penance for some deep-seeded regret for sins.

Scientist brought up the definition of materialist, which states belief in only the physical. But also notice he says "I ain't no Deist" which is just as bold, and takes quite confidence to say and mean. He's denying existence of a god that created the universe and then let it be, with no intervention.

"Recycling the past of / Mid-immediate needs" might refer to religion and other myths. The religious myths originated in Stone Age when humans didn't had long range vision: their only worry was to found food and shelter.

"And through it all we amble forth / The perseverant climb / Our mountains of regret to sow our seeds" might refer to the fact that while religion and myths are always present in human history; science is hardly climbing the mountain of knowledge.

This song is about the philosophical materialism for sure ("It's there for all to see / So don't talk of hit and mystery / With me"), but it talks about the consequences of this materialism, such as skepticism ("I get so full of doubt"), scientificism ("That will deem your common sense useless") and atheism ("The process of belief is an elixir when you're weak").

He is obviously referring to the philosophy idea of materialism. In the history of philosophy there are some basic dichotomies, and one of them is between materialism and idealism. The first (materialism) is represented by natural sciences, and was born with the very first philosopher: "Tales of Mileto", followed by "Democrito of Abdera" and everyone who thinks that the world can be explained referring only to the elements found on it. It surely includes today's Big Bang theory. On the other hand, there's the idealist opinion, whose first exponents are Parmenides and Plato, and is more related to Mathematics and deism. It (very) basically postulates the transcendence of the world. The terms empiricism (David Hume) and rationalism (Immanuel Kant) can be loosely attached to each other as their modern equivalents. However, the problem is more complex than it seems. As far as I'm concerned, Greg Graffin postulates a rational-naturalism, a synthesis between science and common good. That belief is commonly associated with agnosticism and Marxism, although the labels are always misleading.

Materialism is a philosophy adopted by those who wish to avoid a teleological explanation for existence. The song makes a sharp contrast between faith driven perspectives and that of the lyricist. The lyricists admits to being tempted by the other side in the like "The process of belief is an elixir....", yet ultimately is bolstered by his insistence for a natural explanation for his world around him. Ex: 'Don't talk of hidden mystery with me".

I think Greg means the philosophical materialist, because he says "I'm a materialist, call me a humanist" If I'm not mistaken there is something called materialist humanism.

I think he might be referring to the theory that states physical matter is the only reality and that everything, including thought, feeling, mind, and will, can be explained in terms of matter and physical phenomena.