The only down side I've felt is the loss of the Rails asset pipeline. This isn't so bad if you're just building some one-off static site. But when you're also working on a corresponding Rails app (e.g., Jekyll is for the static content, docs, and blog; Rails is all the user-facing interactive stuff), then the duplication of styles and layouts starts to hurt.
So I have been hacking on a bit of an experiment to run Jekyll alongside Rails. My goal is for Jekyll to generate everything in the public directory, and have direct access to the Rails asset pipeline. So far it's going a lot more easily than I expected.
If you're into Jekyll and Rails, take a look: https://github.com/nz/jekyll-rails-hybrid
There are a couple of open questions, and some improvements to asset tags in the works. But I don't see any reason why tightly integrating a Jekyll and Rails app should be more complex than a short readme or blog article. Pretty painless stuff.