Besides the fact that darneys family is responsible for putting dr.manette in jail and darney hasn't shown his love for lucie, there is another reason he doesn't like him. Before Darnay even starts to talk with dr. Manette, dr. Manette knows he is not going to like the conversation. ( he says this to himself) thank you!
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Dr. Manette is actually very fond of Darney. In fact, he doesn't even want to hear about his past in France. He is of course startled at Charles' confession, but he also lives with the couple quite happily. Thus, I think you are wrong in your assumption that he doesn't like him. Remember, Manette allows Darnay to marry his daughter; he didn't have to give his approval, and she wouldn't have married Darnay without it. Manette also works selflessly to clearing Charles when the Republic arrests him.
Tale of Two Cities