I would think that all the comments started with your husband and and all questions should start there.

My son was born with a 6th toe like his dad and his family still said I cheated

Get paternity tests done ASAP. I think your husband started it with the family, but you need to head it off ASAP

You only see the hubbys features in your children. Hubby only sees your features. This is actually very common. If they keep commenting, tell them to buy DNA kits for hubby and each kid for Christmas.

They're probably insinuating that he's gay.

At least three members of your husband's family are assholes.

Tell your husband that it bothers you. He should be willing and able to shut this down. It's his family, he needs to be the one that speaks up. I'm not a Neanderthal or 'Traditional Family Values' kind of guy, but if someone in my family implied my wife had slept with someone else, my wife wouldn't even need to tell me it bothered her. I would be having a very direct, frank, honest conversation with whoever said it, with the expectation that it would never be mentioned again. If it did come up again, they'd get to see the Angry version of me, who doesn't get to come out and wreak havoc nearly as often as he'd like to.

Sounds to me like for some reason his family doesn't like you and is looking for ways to get him to leave you. Not cool.