This is a very interesting question, as this wonderful satire operates on many different levels. Clearly, one central target of Swift's pointed treatise is the unsympathetic response and racist attitude of the British towards the Irish famine, and the way that they appear quite happy to do nothing while thousands of Irish are dying. This is clearly indicated by the shocking and "modest" proposal that the speaker makes of breeding Irish children for a possible food source. Swift is deliberately suggesting the unthinkable and horrific to make a pointed remark about how the treatment of the Irish famine has been just as shocking up until this stage.
However, I think it is also possible to detect another, more subtle message. One of the characteristics of the speaker of this essay is that he makes every effort to present himself as a reasonable, scientific man, who reaches his conclusions on the back of logic and serious investigation. Reason and rationality again and again are hallmarks of his discourse. Swift seems to be communicating the dangers of relying on these characteristics alone when considering other human beings. Just as in the case of the speaker, such people who lean to heavily on speculative reason when trying to find solutions may ignore their own better judgement and arrive at inhumane conclusions, rather than trusting to their common sense and human empathy. Likewise there is a massive danger in dehumanising humans and treating them as statistics or numbers, as this makes it that much easier to treat them as such and forget the shared humanity that is shared between you and them.