The issue with taxes is that they are proportional to how much you make (and for Apple, how much they sell), where as a lot of things that make you more "green" are one-offs.
If Apple's sales go up, but they're having to pay higher taxes to attract those sales, there won't necessarily be a net gain in after-tax profits.
As a contrasting example, installing solar panels is primarily a one-off cost, will probably end up saving you money in the long run, and if it drives sales, the costs of operating those panels don't increase proportionally with your sales.
--
Or, alternatively, maybe Apple wants to be green because that is something the upper management actually care about on a personal level. I don't think it's likely that Tim Cook feels the same way about increasing the French government's tax revenue. Why should he? He's not French. Which, coincidentally, might be the real problem with multi-nationals - at the end of the day, corporations actually are run by people, but most people won't care about more than one or two nations in their lifetimes. Hell, many studies indicate that the average person can't be emotionally engaged with more than a hundred people, much less a hundred countries full of people.
I personally have lived in four different countries, but would say I only care about the success of two of them.