I think Fontaine is bad because of his ideology. He is an unabashed parasite who happily ruins lives and kills just for his own minuscule gains. The more lore reveals about him, the less likeable he becomes, in stark contrast to Ryan who becomes more understandable the more you know.

Fontaine alone being there and being so gleefully evil balances out every single other criticism of Objectivism by saying "well its right about this guy."