@SMickey,
What it means is that there's no significant difference between the two things, circumstances or ideas.
They're both used (spoke/written) equally and mean the same thing. There is no inherent negative interpretation of the phrase. In other words it is not
intended to mean the lesser of two evils , unless someone is actually comparing two bad circumstances. Likewise, if you are comparing two good circumstances it can apply to that as well - it's neutral.