As far as I'm concerned any view justifying the matter is a rationalisation, left or right wing politically; agree or disagree it's certainly nothing to be upset about being called a rationalisation.
My rationalisation is just what I think makes it rational. No negative connotations here. "How do you rationalise that, then?" is where the doubt creeps in.
I think I just presumed someone blogging about being discriminated against for political views would have left-wing political views.
I didn't really realise US academia was so skewed left politically; completely misread the subtext.
So you could use the word "rationalize" neutrally, but most people don't use it that way and don't take it that way.
It seems others commenting on negative connotation are all American, but personally I would only consider it thus in the form of a question:
> Oh yes? How do you rationalise that then?
I would proffer it stems from an assumption that we are rational beings (uh-oh) which may suggest that the very fact it's questionable implies it is incorrect; but we're not rational, people differ - the one thing we all have in common is that we tend to think our own actions rational.
Hence "my rationalisation" is neutral; "your rationalisation" has a negative --ahem-- ex post facto connotation.