I think (to repeat others' points in different language) that to think of rational / irrational as a binary switch is bound to lead to trouble. In other words, I think that the question is whether an action, not a person, is rational or irrational. (Compare with questions of morality, where it is near-meaningless to ask "is this person good / bad?") Why not just "the analysis was rational, and the resulting 'wrong' choice was irrational?"
Once you figure out why you're still picking up pennies even though you know the financial reward is less than the risk then you can determine if it's rational or, if it's irrational, convince yourself not to do it.
(To be clear, there are other plausible rewards to picking up a penny, such as feeling lucky from the superstition. But you only mentioned a financial reward, and the financial impact is negative.)
I sometimes take a stick with horse hair stretched over its length, and pull it along steel cables stretched along a large wooden box. The risks are many, including getting chased out of the house, blisters on my fingers, etc. Am I irrational because I made the wrong choice?
If this is something you are interested in, check out Daniel Kahneman's book.
EDIT: I would like to know the reason behind the downvote. Thanks.
I was the (or a) downvoter. While your point is certainly correct that humans are irrational animals and there is no way around it, that seemed essentially irrelevant to the specific question of whether performing a rational analysis, and then acting against it, should count as a rational or an irrational action. (To be fair, it is highly relevant to the discussion as a whole, just not, I think, to this thread.)
Also, Antonio Damasio's work is an interesting complement/counterpoint to the overemphasis of cognitive rational thinking, and I'd highly recommend it. Descarte's Error is a good place to start, and makes the strong case that rationality is part of an embodied (literally) process upon which it depends.
I certainly hope you don't think that being irrational will help you to be more humane/considerate/farsighted, or that being humane/considerate/farsighted means that one can't be rational.