Actually, having big salaries paid to the do-nothing execs that run those 501(c)3 tax dodges is a good thing. The execs are taxed on those wages and pay medicare, social security and income taxes on those wages. It's the travel, meals and entertainment paid for by the organization for the benefit of the overpaid execs that's the problem.
I think that many of the very rich are the beneficiaries of much more than just tax loopholes. I believe that huge amounts of taxpayer dollars are funneled in to their companies which is what made them rich in the first place.
How many government workers use Windows? And who paid for that? YOU, the taxpayer. And who profited from that? Bill Gates. And that is just a small fraction of the money that went from your pocket into his via the Congress, the IRS, and lots of cronyism.