You're right. I mean if you read the books they're clearly best friends. Sam ends up married and having kids, and Frodo goes off into the sunset. That's how it was originally written anyway, but I remember a lot of snickering in the theater.
I don't think people these days can understand the concept of doing something for another person that you really care about without wanting to bone them. Then again, some of the moments were pretty cringey. "Oh Sam!"
I think people think this because Jon is our "main character" POV in the story and so we sort of identify with him and they think Sophie Turner is hot so they see their interactions in that kind of light due to how they see Sansa. That's just my theory tho.