I was struck by the speed and thoughtfulness of responses from kajsahartig, pekingspring, NickPoole1, richardmccoy and janetedavis, which suggested that the question hit a nerve.
Some of the responses included:
Kasja: Photos from collections have ended up at wikipedia without permission, that never happened with Flickr, could be one reason [and] Or museums are more benevolent when it happens at Flickr, it's seen more as individuals' actions rather than an organisations'?
Nick: Flickr lets you choose CC non-commercial licenses, whereas Wikimedia Commons needs to permit potential commercial use?
Janet: Apart fr better & clear CC licence info, like Flickr Galleries that can be made by all! [and] What I implied but didn't say before: Flickr provides online space for dialogue about and with images.
Richard: Flickr is so much easier to view and search than WM. Commons, and of course easier to upload.Twitter can be a bit of an echo chamber at times, so I wanted to ask you all the question in a more accessible place. So, is it true that museums prefer Flickr Commons to Wikimedia Commons, and if so, why?
[Update: Liam's new blog post addresses some of the concerns raised - this responsiveness to the issues is cheering. (You can get more background at Wikipedia:Advice for the cultural sector and Wikipedia:Conflict of interest.)
Also, for those interested in wikimedia/wikipedia* and museums, there's going to be a workshop 'for exploring and developing policies that will enable museums to better contribute to and use Wikipedia or Wikimedia Commons, and for the Wikimedia community to benefit from the expertise in museums', Wikimedia@MW2010, at Museums at the Web 2010. There's already a thread, 'Wikimedia Foundation projects and the museum community' with some comments. I'd love to see the 'Incompatible recommendations' section of the GLAM-Wiki page discussed and expanded.
* I'm always tempted to write 'wiki*edia' where * could be 'm' or 'p', but then it sounds like South Park's plane-rium in my head.]
[I should really stop updating, but I found Seb Chan's post on the Powerhouse Museum blog, Why Flickr Commons? (and why Wikimedia Commons is very different) useful, and carlstr summed up a lot of the issues neatly: "One of the reasons is that Flickr is a package (view, comment search aso). WC is a archive of photos for others to use. ... I think Wikipedia/Wikimedia have potential for the museum sector, but is much more complex which can be deterrent.".]