Contrary to what Bruce had allowed people to believe, he had in fact been getting paid by SHIELD for his work. He just hadn’t been keeping most of it. He skimmed off what little he needed for clothes (before Howard had supplied him with an entirely new wardrobe and several threats about actually wearing them, that is), food and the occasional goodie for himself. And, because SHIELD provided him with a place to sleep, that left approximately 90% of his pay to be donated to a different charity every week; something he did anonymously.
Bruce was fairly certain that no one knew what he was doing- not that they had a reason to care; it was his money, after all. He just felt a certain compulsion to give back. He helped to fund research into new medications, low cost housing in war-torn countries, provide school books to low-income families; basically any charity which used the money to actually help got his attention. He also worked on the side as a consultant for Doctors in the field, under the alias David Jones. While he didn’t have a full medical background, the biological chemistry of medicine was something he could handle.
It filled his days, anyway, and gave him a greater sense of purpose than he currently had at SHIELD or in the years prior to his recruitment.