Personally I prefer to sleep in futon when in Japan and I do whenever I visit. I will seek out an inn or hotel that has futon.
When I lived there I had a double futon and did not mind putting it away during the day as it was simply a matter of folding it up and placing it in the closet. As I lived alone, I often just left it out as I would be returning later that day and no one would be visiting.
A few of years ago I visited Japan and the in-laws house alone as my wife could not get the time off of work and the air fare was just too cheap to let go. We usually sleep in my wifes room that she she slept in while a child. She has a bed in there and she usually sleeps in it while I sleep in the futon on the floor as I prefer it.
Well, when I went alone that time there were no futon on the floor when it was time for bed. I asked my mother-in-law about it and she thought I had preferred the bed. I said, "No way, mama. I prefer futon!" She was surprised at this, laughed and said, "henna gaijin", strange foreigner, and gladly placed the futon out for me. After all these years she never knew it, my wife never told her, and all the while she thought I was sleeping in the bed while her daughter slept in the futon! Needless to say we became quite close that week I went alone as we talked more than we ever did when I went together with my wife.