How they’re similar: both are organizations trying to accomplish difficult things as well as they can.
How they’re different: Nonprofits take donations; for-profits don’t.
When people draw analogies that have to do with the former, they’re usually valid analogies. Saying that some nonprofits are bad at what they do seems pretty common sense. So does saying that it’s important to figure out which ones these are. So does saying that effectiveness doesn’t always mean low overhead.
On the other hand, anyone who says nonprofits must be “economically sustainable” in the sense of having non-donation revenues greater than costs is simply confused. I won’t go into all the mechanics of why and how it’s possible to provide a service and be worthy of existence while still not turning a profit. Honestly, I don’t think anyone reading this blog needs help understanding that.
Analogies are analogies. They compare two things that are similar in some ways, yet are different things. You have to evaluate each analogy as it comes, and ask whether the things being compared are similar in the way that is being claimed. Otherwise, you’re liable to just start rambling about all the ways in which they’re similar and different. I guess what I’m saying is that I could go for a touch less of that.