Sometimes Medicaid will pay for physical therapy and sometimes they won't.
It all depends on how medically necessary the physical therapy is needed and the state you're in.
Some states offer Physical Therapy as a medicaid benefit while other don't and sometimes medicaid may decide not to cover the physical therapy costs at a later date.
So I would recommend contacting your medicaid provider and asking them directly to be sure if they'd cover the cost of your physical therapy as sometimes they do and sometimes they don't.