That's what I love about it. It is a very classic logo. It evokes for me the idea that it was designed for a high tech company in a sci-fi film. Like Cyberdyne Systems or TYRELL Corp.
I was instantly reminded of the OCP - Omni Consumer Products - logo from Robocop, and yes, I also like the slightly retro-future feel.
As much as it's entirely irrelevant to Vagrant-as-a-tool itself, I'd love to see a whole 'brand identity' in the same theme. It's a small thing, but it makes me slightly happier when the tools I use have a little bit of character to them. (See also: Github & Octocats)
I suppose my only question is if you plan on redesigning the Vagrant Docs website to be more like your attractive company landing page.