Okay, let's compare their misdeeds to their positive influences. They've given a lot of money to charities, and indeed do a lot of charitable work themselves.
But then if you look just a little bit closer, nearly every one of their positive endeavours is coloured by ulterior motives. From crisis pregnancy centres that basically bully women into not having abortions and then provide them with little-to-no medical care to rape counselling that doesn't include the morning-after pill to forcing people to listen to a sermon before they can have some food, it's really questionable whether any of the good things things that the RCC does are actually as good as they seem. And since their accounting practices are essentially a black box, constituents have no idea how much of their money even goes to charity. The "charitable" donations of the RCC may actually be draining money away from other organisations that would spend a much larger percentage of their donations on actual charity, in which case the "good" done by the RCC is actually counter-productive.
Now let's get to the bad. There are a lot of things I could mention, but frankly, the pope's public stance on condoms in Africa has the potential to kill enough people that that alone easily cancels out all the good that the Catholic church does, even if we assume the best and give them credit for all of their charitable endeavours being legit.
In short, the balance is "maybe possibly feed a few poor people after forcing them to listen to a sermon" versus "kill a few hundred thousand people". It's not even close.