Everyone uses public infrastructure. That's what makes it "public infrastructure". Should we raise your taxes to 80% "because you use the roads that are built by taxes"?
(I'm asking as a proponent of progressive tax rate, just not for this reason. So I'd like to clarify)
A flat tax, then, is actually quite regressive, rather than neutral.
Speaking in terms of companies, though, there is also a question of proportion vis a vis size—bigger companies and their employees tend to cost taxpayers quite a bit more than small businesses. There are no giant Twitter-like subsidies for five-man firms, for example. Larger firms are much more likely to make use of legal infrastructure, to need regulation, and to have the power to seek accommodation by the government for infrastructure needed for their given business.