Wayne Enterprises probably owns, operates, and/or donates thousands of buildings, many of which house charitable organizations. WE is huge and has hundreds of offshoot companies - It's reach and scope is only eclipsed by LexCorp.
Unlike the Marvel Universe, the DCU is a place where people build museums and statues to their heroes - they like superheroes, for the most part, until the plot demands that they don't - so it's certainly not unlikely that the third richest man in the world would throw out some bucks to a fledgling group of crimefighters to get them started.
Indeed, in the DCU, the super-rich fund superteams about like they buy NFL teams in our world. It's a status symbol, contributes to the common good, and it's probably a huge tax write-off.
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