His "Product Red" brand was set up to look like a charitable organisation, but it was super dodgy. They weren't transparent about how much of their income was spent on the causes they supported, and there were reports that claimed that they spent more on advertising and promotion than they contributed to the actual causes. It's hard to assess though, because nothing about it was open to scrutiny.
Also, U2 basically cost Negativland their record deal when they sued Negativland for sampling some U2 work. It should have been covered under fair use, but the label didn't have the money to fight it, so they settled out of court and dropped the band.
Oh and Bono is perfectly happy with using tax havens to avoid paying tax.