I'm not trying to justify them because they are too high regardless, but it does sound like it's not an apples to apples comparison. Their accounting rules are much stricter due to state law, so some of the things NDSU doesn't count towards athletics, JMU(and others) have to.* And JMU is very limited in what monies they can use to support athletics, so they have to use student fees in cases where NDSU would split it between student fees and other institutional funds.
Again, I believe they are still too high with their institutional support, but it's not as huge a divide as the raw numbers would indicate.
*I'm thinking things like grounds maintenance, utilities and the like. For example, I expect NDSU doesn't break out how much it costs to heat the SHAC(since the campus uses steam heat) and "bill" the athletic department for that.