Are you British? (I'm picking up on the 's', not sure if you're just quoting me).

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?

The answer to which is a statement of facts - how it is that I deem whatever 'that' is to be rational.

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.