Except... they sometimes don't appreciate the breadth of the 'job'. For agency A to get their 'job' done, using fonts ABC works just fine. But now when that same font needs to be use in other areas they're not licensed for, their client either can't have the same brand experience in other media, or has to pay a heftier price to do so, or is running afoul of the licensing terms.
This is a couple steps above people just going to google images and grabbing whatever images come up for their own websites. Still same licensing/terms-of-use problems, just with a higher price tag attached. And somehow, when people are using big fancy agency XYZ, they think (rightly?) that the agency always knows what they're doing (often they do, but sometimes they don't).
Agreed, I just think the pendulum hasn't swung far enough on the open direction, because of the relative newness of the tech. In other words, it seems that branding agencies sometimes use proprietary type families out of habit and ignorance, not because they've evaluated the tradeoffs and made a careful choice.
I think their choice is more rational than you give credit for. While there are now quite a few good freely available fonts for use on your blog or small business site, there are still few, if any, open font families that offer the same breadth as good commercial offerings. If you're a large organisation, bringing in an agency to create overall branding guidelines that will apply to everything you produce from slideshows to printed brochures via web apps and business cards, it would be foolish of that agency to suggest typography that didn't offer enough range to be future-proof.
Basically, just that it's useful to remember that large organizations, as much as they'd like to be, aren't always as homogeneous and cohesive in branding and approach as they'd like to be.
The following is also anecdotal: I work in the contact center world, and it's pretty surprising just how isolated and disconnected some companies are when it comes not just to brick and mortar vs e-com, but e-com and it's call centers.
Add in more prefaces/cya's that I haven't done formal research on the subject where necessary :)
The two should also not be opposites. There should be room for commercial open-source typography.
If it isn't the typography world is going to be poorer - coz designing good fonts is a hard, skilled, time consuming task and not everybody has the time and inclination to do it for free.
(Otherwise we're going to see more things like the recent non-OSS fork of Merriweather for example http://ebensorkin.wordpress.com/2014/03/02/the-pro-merriweat...)
Because either it solves a lot of problems, or it creates some new ones and basically makes it super easy to fall into a license trap.