I tend to use C# minor a lot as well. I think it fits quite naturally under the hand. Basically, both C# Aeolian (the plain minor scale), as well as the harmonic minor scale, are very ergonomic. Contrast this with E harmonic minor, or B harmonic minor, or D harmonic minor, where reaching the leading tone with the ring finger isn't so intuitive. However, for C# harmonic minor, you just have to move from the thumb to the index finger. So, you can easily flit between natural minor, harmonic minor, and even (I think) melodic minor, and all of them fall under the hands quite nicely. In general, key signatures with more black keys are more ergonomic. At least in my experience, C# minor is a pleasure to work with.
There are a few other key signatures which are pretty ergonomic, Ab minor comes to mind, both the harmonic and melodic variants have a very similar pattern to C# minor. Maybe C# is used more because it sits right near the center? -- This one might just be convention.
Edit: F# minor is also quite good.
ETA. It could also be because of the modulation possibilities. From C# minor, you can modulate to C#/Db major, or E major, both of which are pretty good. You could also have sections in F# or G#. Also, F# and G# are the 4 and 5 respectively, and it is very comfortable to play those chord configurations, and you can also play them really fast, quite easily, due to the way you have one white key and two black keys, which allow for stuff like really quick arpeggiation. So that is an added convenience. Just a thought.