Hamlet is conflicted. It is clear that they cared about each other prior to Gertrude's remarriage--she worries about his depression, and he worries about her lack of it. But though Hamlet wants her to be more morally upright, he does not wish harm to come to her and his father's ghost forbids him to punish her.
Hamlet is no more "in love" with his mother than Ophelia is in love with her father. The sexual references are no evidence of that--not once does he make reference to a sexual union between him and her, or even pun with them. His comments focus on how easy she is and fickle. (On the other hand, he does make sexually suggestive comments directed at Ophelia, asking her if she means "country matters" and if he should "lie" his "head upon" her lap).
Hamlet's sexual innuendo calls into question Gertrude's morality and her faithfulness. In this, he insults both her and Claudius, for they have both broken with protocol in their overhasty marriage. Nothing in the text indicates he is concerned about her faithfulness to him; it is her lack of faithfulness to his father that angers and upsets him.
This is a powerful argument in favour of his filial love for his mom because if he were indifferent toward her, he would not feel as deeply hurt, confused, and betrayed as he does.