http://guides.rubyonrails.org/
Which bits did you find were magic? The bits of convention I can think of you'd have to know about are:
DB naming conventions - these are used so that it can do joins etc easily behind the scenes, they're pretty simple so not a huge problem I find.
Rendering at the end of controller actions - it'll render the template with the same path as your route - again relatively straightforward.
Class loading - lots of things are loaded at startup time, so that you don't have to include files - I have mixed feelings about this, it feels easy and simple at first, but could leave you unsure where code comes from or which methods you can use in which files (e.g. view helpers). Definitely more magic.
One other area which does lead to real problems is that rails sites often use a lot of libraries in the form of gems - this leads to unknown, sometimes poorly maintained or inappropriate code being pulled in at runtime, and makes it far harder to reason about things like say authentication if using a gem. This is my biggest complaint with rails - lack of transparency of code paths when using gems like devise, paperclip etc but it is unfortunately quite common in web frameworks
They actually got rid of quite a few bits of method_missing madness I think recently so that magic is gone at least (all those magic find_by_ methods are deprecated or removed, not sure which as I never used them). I haven't found the conventions get in the way much as it's something you learn once and can apply anywhere, but completely understand why someone might object to some of the magic setup for helpers/rendering.