Well, how about we flip it: why are secular organizations not recognized for the work they do? I mean, why are religious institutions getting all the credit as if they were inherently more virtuous?

The only advantage religion has is its active community that propels initiatives as part of a grand ideal. I don't think the actual work would go undone if the project had already been established from the overwhelming support of an existing secular community. Helping others is, after all, human nature.

they are no different than anyone else doing those things for their own reasons

They are absolutely different, because in some major religions, devotion is rewarded or promised heavily in the afterlife, which creates a great incentive. These people are more likely to become radicalized or extremists, often going out of their way to impose their worldview on others through harassment, aggression, or influence. I'll point to Mother Theresa, who inflicted so much pain on others when she thought she was doing good, often withholding pain medicine and other treatments. She said suffering is what God intended, and so she did... unto others.

My point was not to say that non religious people are all saints, but to balance out your previous point where you praised religion without nuance.

Of course the common denominator is people. And it’s pretty easy to see how religion is a powerful tool for these people to do evil, wouldn’t you say?

I think you're not taking into account its hierarchical nature founded on unquestioning obedience, and the unearned & inherent facade of trust it has for some people. These tools aren't available for the non-religious which is very enabling if your goal is to exploit. And exploit they have.