I think Mr. Mayer is commenting on what he believes to be a major source of animosity and separation of human cultures.

Belief (be it religion, patriotism, pride, etc.) can provide mental and physical security for those who participate in it. "belief is a beautiful armor". It can unite many people for a cause and allow great things to happen.

the line "but makes for the heaviest sword" means that the
Belief can be double sided... although belief can unite many, it can be used to draw a clear line of separation between cultures, social groups, even when separation is not beneficial to either. with the line of separation drawn, the negative actions of a few can be associated with an entire demographic, blame can be more easily placed, anger and fear are given a focal point and "enemies" can be identified. Misused, belief can be blindly destructive to our society

"what puts a hundred thoudand children in the sand" obviously refers to the Iraq war, but the songs meaning reaches much farther than that.

He wants us to see that when try to force our ideas and beliefs on others, the result will be conflict. Moreover, when you convey your ideas though force, can you really expect a positive reception? as identified in the first stanza

Is there anyone who
Ever remembers changing there mind from
The paint on a sign?
Is there anyone who really recalls
Ever breaking rank at all
For something someone yelled real loud one time

I think he is also questioning support of military action, on both sides of the war... both sides are victims of lies about the other, lies used to build cases for war, reasons for hatred.

neither side is right or wrong, we are just fighting for our beliefs