Absolutely. Some nonprofits are scams but those are just the ones that have armies of collectors on the streets showing pictures of starving kids and asking for your bank details. But they stay obscure and out of the limelight (eg advertising) because being obscure is what makes them from being taken down.
I think the big NGOs are no longer effective because they are run as the same corporations they fight and are influenced by the same perverse incentives. Like eg Greenpeace.
But in general I think non profits are great and a lot more honorable than for profit orgs. I donate to many.