I think Abra is most likely right. You could call a store that sells futons and ask them.
Running a humidifier is the right thing to do. Winter air is dry. I have one running in my bedroom and I feel much better.
Basements tend to be damp. Seems at odds to dry air. There is an inexpemsive device that will measure the humidity. If the humidity is high enough you could stop running the humidifier. The Internet has information.
If the mold is the result of the humidifier being too close to the futon, you could move it further away. What kind of humidifier do you have. The warm steam ones always left water on the walls and floor, for me. I now use an electronic cool mist one and it's great. No extra moisture on walls etc.
Have you checked the rest of the room to see if mold is building up anywhere else?
As to water proof mattress pads you can buy "rubberized" ones at Fred Meyer. Both sides are a soft flannel. I've slept on them and only noticed extra bulk when it got bunched up.
I've also purchased the type of pad they use in hospitals and nursing homes at thrift stores for just $2-3. They are larger and some have fabric "wings" that go under the mattress to hold the pad in place. They have more than one layer of fabric on both sides. I think the pad from FM bunched up because of my size and weight. I don't remember it bunching with my grandchildren.
I also think that you should throw the futon out. That mold is most likely thru out the stuffing and would be impossible to get it completely out. Mold is toxic, more so for some than others. Baby's systems are still maturing and I'd be concerned that the mold could make him ill now and if not now will enable his system to develop an allergy.
My cousins had to move out of their house because mold built up in the walls. I've read that this has happened to many families.
Their symptoms were chronic and they felt like they had a cold with headaches.