Well you made me take a longer look at goodwill than I would have otherwise. They employ over 7,000 disabled people under Section 14(c) Subminimum Wage Program, an intentional loophole in the Fair Labor Standards Act of 1938. Some of these individuals earn less than $0.20 per hour of work.
This is considered Job Training, and isn't meant to be a long term position, but of course that is how it's used. Of those 7,000 workers, Goodwill was only able to place 500 or so into another job (essentially graduating from job training) in 2011. This isn't a small amount of trained workforce, but it's clear that the majority of the people being "trained" are not on a path that will take them out of subminimum wage.
Be that as it may, Goodwill also helps these people apply for federal assistance, and none of them are homeless or hungry. They aren't supporting themselves, and Goodwill isn't supporting them, but because of Goodwill's effort they are surviving and have something to do that keeps their mind and body active - and the value of that can't be easily assessed.
They are their own charity, they don't donate to other causes (not substantially, anyway). Their entire mission is to provide job training and job placement to the disabled, uneducated, inexperienced, or otherwise face employment challenges, and they claim about 88% of all the funds they raise go to that. I haven't delved into the numbers deeply enough to know how that 88% figure is derived, but if it's honest, then they are a decent charity.
However, there are some serious questions about the loophole in the minimum wage. These can be considered discriminatory - the federal minimum wage protections that everyone else receives do not depend on our productivity.
Here's one article that is critical of Goodwill, from which most of my numbers come:
http://www.huffingtonpost.com/john-hrabe/the-worst-corporation-in-_b_1876905.html
Charitywatch rates them an A:
http://www.charitywatch.org/toprated.html#disabled
Google knows everything:
https://www.google.com/search?q=how+does+goodwill+spend+its+money
Goodwill, of course, has its say:
http://www.goodwillakron.org/about/environmental/what-happens-to-your-donations
Snope's article has a lot of good links to charity watch organizations and charity lists that delve pretty deep into what each organization is actually accomplishing:
http://www.snopes.com/politics/business/charities.asp
Overall, the CEO salary doesn't bother me, for the reasons you list, but the subminimum wage issue bothers me, and should be examined carefully by congress to determine if it still has a good role to play in our society, and actually serves its intended purpose without too much abuse.
Regardless, of all the ways I can dispose of my junk that still has some value to someone, somewhere, Goodwill puts it to better use than any other place I might toss it. Further, I buy most of my clothing there, so even if it weren't a non-profit, I'm still benefiting from their stewardship. If I'm benefiting due to subminimum workers, though, and if that is hurting them, or simply not helping them as much as it could be, then I'd not be happy.
At the moment I don't see too much cause for alarm, but I'd like congress to take another look at it. The law is over 75 years old, things have changed economically enough that we shouldn't assume it's the best idea.