I would hesitate to say that the issue is a "hack". Or indeed that threaded solutions are necessarily superior.
The situation is a result of design decisions used in the interpreters of languages like Ruby and Python.
I work with Ruby, so the details may be different for other languages.
BUT ... essentially, Ruby uses a Global Interpreter Lock to prevent threading issues:
http://en.wikipedia.org/wiki/Global_Interpreter_Lock
The side-effect of this is that to achieve concurrency with frameworks like Rails, rather than relying on multiple threads within the VM, we use multiple processes, each with its own interpreter and instance of your framework and application code
Each instance of the app handles a single request at a time. To achieve concurrency we have to spin up multiple instances.
In the olden days (2-3 years ago) we would run multiple mongrel (or similar) instances behind a proxy (generally apache). Passenger changed some of this because it is smart enough to manage the processes itself, rather than requiring manual setup. You tell Passenger how many processes it can use and off it goes.
The whole structure is actually not as bad as the thread-orthodoxy would have you believe. For a start, it's pretty easy to make this type of architecture work in a multicore environment. Any modern database is designed to handle highly concurrent loads, so having multiple processes has very little if any effect at that level.
If you use a language like JRuby you can deploy into a threaded app server like Tomcat and have a deployment that looks much more "java-like". However, this is not as big a win as you might think, because now your application needs to be much more thread-aware and you can see side effects and strangeness from threading issues.