The biggest concerns I've heard from other researchers (ie, professors) has to do with being beaten at a publish. I think that as long as your paper itself isn't easy to find pre-submission, then you're okay, especially if nobody will really understand what you're doing anyway. So, I'm not too nervous about the prospect. It's just code for now.
Unfortunately, even if scientists release their own code, it's often just a small part of the big picture. In engineering, at least, MATLAB, Mathematica and commercial Finite Element packages are everywhere. My own project uses MATLAB and COMSOL in tandem, meaning that what I wrote only really serves to glue a bunch of completely closed algorithms together. Personally, I'd love to see a completely open, usable and documented FEA stack (which would ideally include an adaptive mesher, some FEM algorithms, a post-process visualizer, and both a gui and a not-shitty scripting API).