IANAL and this isn't the legal justification. But US corporations are treated with rights similar to actual people with slightly better treatment in some ways, slightly worse in others.

So: morally corporations should pay income tax because all persons are subject to income tax. And we have decided that corporations are persons. It's no more a "bonus" tax than it is a bonus tax when I pay my accountant and she also has to pay tax on that income (even though I have already paid tax on the money).