Nelnet customer service is great, so call or drop them an email. One thing I have found is that you can't make principal-only payments, so any extra payments just push back the due date of the next payment.
I don't think that is legal.
From their website: "Per regulations, all payments are applied to fees first, then interest, and finally principal unless your current repayment plan is Income-Based Repayment. In this situation, your payments would first be applied to interest, then to fees, and finally to principal. If you send in a payment greater than the minimum amount due, the additional amount will automatically be applied to your principal balance after all outstanding interest and fees are paid. Nelnet cannot apply payments in a way that does not conform to regulations."
So yes, it's applying towards principal, but it's not a principal only payment (the way you can do with a mortgage). I had a car loan with Toyota a few years ago that was exactly the same - it's how simple loans work. In the long run, you are saving on interest because you are shortening the length of the loan.