Schlesinger's column cites Wayne's parents' construction of a subway as proof the family cares about those less fortunate than them. There is no doubting Thomas Wayne is supposed to be a good man possessing a deep-seated desire to "give back" to his community. But that is far from inconsistent with libertarianism. The gifting of such an asset by a private individual could just as easily be used as evidence that "public" goods like transportation need not come from government at all.
In the third installment, Wayne realizes his immensely valuable fusion reactor could be weaponized if allowed to fall into the wrong hands. He refuses to put it into production, though it means enduring the loss of his fortune. If anything, Wayne proves that even for the wealthy businessman, there can be more to life than money.
The Batman is much more a libertarian archetype than a repudiation thereof. He may not be a hero of the Randian variety, but Bruce Wayne's willingness to sacrifice for the good of others is a cinematic depiction of the best that free humans are capable of. His heroics underscore one of the foundational precepts of the libertarian movement. It doesn't take big government to make the world a better place—it takes people choosing to do the right thing.