Why was Swift criticized for the ideas satirized in Gulliver's Travels?

Swift was criticized for his satire because the novel itself is highly critical of the English government and English customs, the country's religious struggles, the monarchy's handling of those struggles, and so forth.  For example, the Tories and Whigs, the two main political parties in England during Swift's life, are satirized by the Tramecksans and Slamecksans, respectively, of Lilliput.  The Tramecksans wear high heels on their shoes, and the Slamecksans wear low heels.  This makes them seem quite ridiculous, and Swift goes on to not-so-subtly criticize King George II for his sympathies for one side and style of shoe.
In addition, the debate between the Big Endians, those who believe one should crack their eggs on the wider end, and the Little Endians, those who believe one should crack their eggs on the smaller end, satirizes the divide between Catholics and Protestants, respectively.  Gulliver says, at one point, "that eleven Thousand Persons have, at several Times, suffered Death, rather than submit to break their Eggs at the smaller End."  In characterizing the differences between Catholics and Protestants in this way, Swift makes the wars fought over religious disagreement seem ridiculous.  Why should one be willing to die for something as minor as which end to crack one's egg?  Swift's answer seems to be that one should not.  Either way, you end up with a cracked egg; likewise, whether you are Catholic or Protestant, you still believe in the same God—does it really matter whether the communion bread is symbolic or actually miraculous?  Again, Swift seems to suggest not.  This kind of satire would certainly draw criticism from those who saw the differences as crucial.