Yep, not sure where this perception of "nobody's using it" comes from but I have been using it in 2 different companies in the last 3 years as well with nothing but love. In fact, if it were the case that "nobody's using it for good reasons", maybe we should ought to know the reasons?
Been using opsworks for about a year now and while it has very significantly streamlined our provisioning/deployment tasks, "nothing but love" is not quite how I'd describe it.
You could code up something in the deploy hook to select the master node (mostly the first instance in the layer) to run migrations and you could disable the "Run Migrations" when you deploy. I do this for the Rails app in my company.
I actually solved this with our custom deploy script. We choose the machine that runs the migrations.
The necessity of building and maintaining a custom deploy script is the biggest wart for us (though I admit that the API is pretty good, and said script has not had that much maintenance overhead).
Those of use contributing on the Guide so far have generally been companies where it's not used. I'd love to see a contribution (a few bullet points and/or links) that better covers the basics and reflects how/when it's useful.