Consider the mortgage interest deduction, for example, as we approach tax day. Or the one for charitable contributions. Or a host of other examples.
These policies assume that home ownership and a healthy non-profit sector are good for individuals and society. Their architects and defenders (which, yes, do include vested interests) believe the social and economic benefits of promoting these behaviors offset the loss in government revenue.
It works the other way as well, with high taxes on undesirable behaviors. The primary motivation for higher taxes on, say, cigarettes, should not be to permanently increase revenue, but to discourage plainly destructive behavior.