<p>I'm starting to learn ruby. I'm also a day-to-day C++ dev.
For C++ projects I usually go with following dir structure</p>

<pre><code>/
 -/bin &lt;- built binaries
 -/build &lt;- build time temporary object (eg. .obj, cmake intermediates)
 -/doc &lt;- manuals and/or Doxygen docs
 -/src
 --/module-1
 --/module-2
 -- non module specific sources, like main.cpp
 - IDE project files (.sln), etc.
</code></pre>

<p>What dir layout for Ruby (non-Rails, non-Merb) would you suggest to keep it clean, simple and maintainable?</p>

Why not use just the same layout? Normally you won't need build because there's no compilation step, but the rest seems OK to me.
I'm not sure what you mean by a module but if it's just a single class a separate folder wouldn't be necessary and if there's more than one file you normally write a module-1.rb file (at the name level as the module-1 folder) that does nothing more than require everything in module-1/.
Oh, and I would suggest using
Rake
for the management tasks (instead of make).