Swift is indicating in 'A Modest Proposal' that we often put theory and economics way before humanity and the individual. We can see the effect of blind theory over humanity throughout history: think of the 'battle stategies' of World War 1 where soldiers from either side walked towards each other across open land, both sides firing weapons. Hitler's theories surrounding the advantages of an Aryan race ignored the atrocities it took to realise the flaws of this pseudo scientific idea. Swift's satire was sadly not understood by all.
I agree with what the first post says, but it does not seem to identify a specific human fault the way your question asks for. I think that Swift is indicating that greed and callousness are human faults. I think that he is saying that the English (and the rich especially) are mistreating the Irish because they (the English) are greedy and do not really care about the Irish. He is saying that the English care more about money and wealth than about human beings. This is the general point he is making -- that many human beings, like the rich English are greedy and uncaring.
"A Modest Proposal" is that Swift makes in his proposal is that a solution for the extreme poverty of the Irish would be for the Irish and the English to eat the children, especially the babies. He lays out all of the completely logical reasons why this would be beneficial to everyone. CLEARLY, the satire is about the way the English treat the Irish, taking economic advantage of the small island, and allowing the continuation of the poor economic conditions there. Towards the end of the piece, Swift actually lists five or more other solutions (which are clearly intended to be the REAL solutions) to the problem. This piece must be read for the satirical tone, but it is so convincingly written, people then and now ask themselves, "is he serious?"