The pediatrician makes a lot more then $0.25/vaccine. Vaccines and the related visits that go hand in hand with the vaccine schedule makes up the majority of pediatrician's income. So there may not be too much money made on the manufacturer's side but distribution there is plenty.
Also with vaccines being immune from lawsuits that decreases the risk that the manufacturers have for any losses. So that smaller profit is almost a guaranteed profit.
RE: Flu Vaccines Elevate Air-Borne Flu Particles by 630% - USA National Academy of Sciences Publication