R.B.
My daughter is in 6th grade and still does NOT like to use the bathrooms at school. She will use public bathrooms (at the mall, on an airplane, etc), she just doesn't like the school bathrooms.
Perhaps he doesn't care for the smell of the cleaner they use(or perhaps there have been accidents and he can smell them?) I wouldn't make a big deal about it, as long as he doesn't have accidents and will go to the bathroom when he truly needs to. Or, are they open / communal toilets for all to see?