I'm guessing that your question is prompted by all the time that Huck and Jim spend naked on the raft together. You may also be puzzled by the term of endearment, "honey," that Jim uses towards Huck. What you should remember is that there is a big age difference between Jim and Huck. Jim watches over Huck, is loyal and protective, and loves him. Calling him "honey" indicates his affection for Huck, but not in a sexual way. It's also common to address someone as "honey" in informal situations.
And now for the time on the raft: Twain is commenting on Eden, not on homosexuality. You may remember that "everything is free and easy" on a raft. There's no judgement, no rules, just floating and equal respect. The nudity helps symbolize the equality between Jim and Huck. You may recall that Adam and Eve were naked before they ate the fruit and recognized their difference from eachother. Every time Jim and Huck hit land, they get dressed again, indicating that difference once again matters.