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.
My (anecdotal) experience has been that given a large enough organization, you're probably going to run into a lot of subsets of the organization that just don't know any better or aren't aware of the company branding strategy and guidelines. It's probably a reasonable bet to say that most of those groups won't be creating public facing content, but I've seen it happen often enough before. Not a broad study, but an interesting note.
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 :)
Perhaps. I can certainly appreciate that a brand designer may be worrying about a wide range of print and advertising media, and in that grand scheme of concerns the web isn't all that important.
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.