I've recently become somewhat addicted to "Stack Overflow":http://stackoverflow.com, and I have noticed some areas of confusion with using Ruby on Rails. Convention over configuration and awesome magick are pretty foreign concepts in most of CS, so the confusion is quite understandable. The Rails community also seems to have a love for demonstrating simple applications being created simply (Blog in 5 minutes, extreme!) and complex corner cases solved through advance techniques. There isn't much in the way of middle ground.
If you are planning on doing a lot of Rails and are okay with buying dead tree books, you should go buy The Rails Way by Obie Fernandez at your soonest convenience. It is worth its (considerable) weight in gold
The following are what I've observed to be among the hardest issues for people moving from idealized Rails applications to the realities of actual websites. I will try to mostly avoid the issues of separation between the levels of MVC and any of the philosophical opinions of DRY.
h3. Dependencies: How to make Rails find your classes.
Starting out, Rails is amazing at automagically including everything you need to make the code run without any need for @require@ or @load@ lines. Things get a little more confusing when you write your own code and find that it is not being included where you expect. The key here is that Rails uses *naming conventions* to handle code loading.
The naming convention is that class names are in CamelCase and the file containing them are named using underscores.
Classes that serve as models, views, controllers, or sweepers should go in their properly named folders under @app/@. Other classes should either be placed in @lib/@ or factored out into plugins.
It is worth noting that files are only loaded when the class name is referenced in the code. Whenever an unknown class name (or any constant) is used in code, Rails attempts to find a file that might define it (according to file name) and then loads it.
@config/routes.rb@ is kind of a mess. This is what you need to know.
h5. Connect a url to a controller action
This makes http://foo.com/foo/42 go to FooController#bar with params[:id] = 42
This does the same, but only for GET requests
This validates that params[:id] is a number (/foo/42 will match, /foo/baz will not)
h5. Named routes
Linking to controllers through @link_to "click here", :controller => 'foo', :action => 'bar', :id => 42@ is cumbersome. Named routes allow you to reference this same path with @foo_path(42)@
All previously discussed options work the same for named routes.
h5. RESTful resources
If you use REST (and you should), routes get a whole new load of magick.
That's it for now. The API (http://railsapi.com) is a great reference for other issues that might come up.
fn1. Ron Paul has proposed using copies of The Rails Way as the basis for US Currency.