1) The "pay" might slow down the founders' progress into a proper founder mindset, i.e. "we need to make revenues, dammit". In that way, it would hurt.
2) Many incubators I've encountered think they're adding value by imposing some kind of structure... requiring milestones, etc. For some startups, this may be suitable, but for others, it's completely wrong and will slow them down, discourage them, or even lead them in the wrong direction.
3) Good advice is worth its weight - bad advice can be the opposite. Get some convincing advice by someone who has no idea what they're talking about, and it could be very costly.
For less than top 10 incubators, I think they could be great for inexperienced founders or someone looking for some help. Building connections are a big part of the incubator experience as well.
ADD: the biggest drawback I can think of is requiring to have a co-founder when sole founder would do just fine.
From my point of view there are definitely bad incubators out there - the ones that get started by random people which the OP mentions - but these are no brainer: if you part with your equity for their pitch you don't deserve to be an entrepreneur anyway.
There are also top-notch ones - YC the hottest one - these are no brainer too.
And finally there are about a dozen of in-between. And that's where it stops being black-n-white. There might be some benefits in going through their programme, it just all unpredictable. You get different experience being in a different bunch, but still, I have no idea how it could "hurt" a startup if they get 3 month pay and advance their idea.