Very curious to know this, since it doesn't look like the BFR will utilize centrifugal force to emulate gravity as far as I know.
- Make trips that carry humans as short as possible.
- Frequent physical resistance exercise, as on the ISS.
- Build extra muscle mass and strength before departure, to help counter losses during the trip.
Perhaps mission planners will also look into the idea of putting a slight spin on the BFS while in transit. I haven't seen any reports of that yet, though.
IMO, it's likely that the low-gravity environment on Mars will also have an adverse effect on human health in the long term, without focused efforts to counter it.