As FreeGirl2006 notes, nonprofits can have taxable income. The 990 form is the form used to communicate the income from a for-profit enterprise within a tax exempt or nonprofit company.
As I've said in the past, none of these random bits of paper are actual financial reports. Real transparency would mean releasing an audited financial statement every year. They've never done that, nor are they required to. However, many churches believe that financial integrity begins with transparency, and thus they release their financials.
If you really want to force change in the organization, pressure them to provide their flock with real information.