Let's just look at this quickly. The Blue Water last year spent $1.1 Million operating 2 daily trains. $1.1/365/2=$1,506 per train in expenses.
Each excursion train had more than 800 people on it. 800*$89=$71,200
Even with pay NS for the pilots and assuming that they couldn't get NS to give away track rights for the run, the odds fully favor that these trains made money. It's not going to balance the budget for Amtrak; but I rather doubt that they lost any money on this. And it was great publicity too!