It's Jane's personality that is at issue. I believe Darcy sees her very much as a soft, pliable young woman who, if not mercenary herself, will act so under the direction of her mother. Remember the comment "She smiles too much." That, I believe makes her appear somewhat false as though her feelings are superficial. When you factor in that he has never sen any sign of emotion from her - she always appears quite complacent and content - it is hard to fault his analysis.
I would also point out that Bingley himself, who should know her better than anyone, can be convinced that she holds no affection for him.
I won't quibble about his arrogance.