In the end it’s certainly because at least some of the executives making donation decisions are bigots, but here’s my attempt to come up with an explanation for why the corporation as a whole would view these donations as strategic:

They perceive that electing Republicans is beneficial for their business, and the Republican party uses bigotry to motivate their base. Hate against queer people is the R’s cause du jour. Funding hate groups means those groups produce more bigot propaganda, which makes the Republican electoral strategy more effective, which makes it more likely that Republican candidates will be elected who are perceived to be more amenable to deregulation that would allow banks to increase profits at everyone else’s expense.

So from this perspective, banks see queer people as a group they can extract value from, both through rainbow washing initiatives to attract them as customers and talent and (as seen here) as a target they can attack in pursuit of political power, which is equivalent to profit.