Loyal site readers are probably aware that one big pet issue here concerns the reporting of financial information about college athletics. Journalists who cite the Department of Education's Equity in Athletics database, like Brett McMurphy (formerly of AOL Fanhouse), Kristi Dosh for Forbes.com, and a recent ESPN Outside the Lines piece do an incredible disservice on this issue in failing to distinguish between revenue sources, which paints the rather misleading picture that athletic departments largely break even or are profitable. The NCAA has called the Equity figures "meaningless." They're not making money if colleges have to subsidize them. The best way to go is to file an open records request with each athletic department for their annual NCAA Revenue and Expense, which unfortunately is little help for the likes of private institutions, and Pennsylvania's "state-related" universities.
When comparing Rutgers in 2008 to 2009, there isn't much of a stark difference. Rutgers is in the unfortunate position of giving, relatively, a very large subsidy to athletics (which does not necessarily equate to football only.) That needs to fall back over time, and may as the economy improves, but did not in the 2009-2010 calendar year. The critical "Direct Institutional Support" figure actually jumped by 500k, but was a smaller percentage of the athletic department budget. Real revenue was up, but the problem is that expenses (specifically, facility costs) jumped even more.
A recent Star-Ledger piece provides additional context for the ticket revenue figures. Student fee increases added more revenue, with clear positives being a jump in contributions (does the figure disparity there owe to NCAA accounting standards?) and more NCAA/conference revenue. That does not prove that expansion caused bumps in revenue and expenses, but it's by far the most intuitive explanation. Stadium expansion bumped up football attendance, and provides numerous benefits (see previous link), but also appears to have slightly exacerbated the athletic department's near-term financial deficit in 2009.