It seems some of the criticism is because it's not based on the latest scholastic works about life in the middle ages, and that it's derivative from a conglomeration of other sources (Durant's 11 volume History of Civilization is one example) with little original research.
Defenders of Roman Catholicism may also be particularly offended by descriptions of church and papal excesses (Lucrezia Borgia's reported incestuous relations with both her brother and her father the Pope, wild bacchanals in the Vatican, bestowing Cardinalships on the bastard sons of high ranking clergy members, selling indulgences to forgive those already dead, etc).
Nevertheless it is an interesting and illuminating read; for example, the Pope's refusal to grant Henry VIII a divorce from Catherine of Aragon (after a 5 year wait) was because he did not want to offend Charles V of Spain (her cousin), as the Pope was promoting him to assume the crown of Holy Roman Emperor in hopes that he would squelch the rising protestant movement in the German territories.