If the company didn't net more than $250,000, the owner would not have his taxes raised under Obama's plan. The reason Mr. the Plumber used the figure of more than $250,000 net was to show that he would be hurt by Obama's plan. He doesn't use the word, "net". He uses the word, "makes". The money that is "made" by a company is its net profits.

A company doesn't "make money", for instance, if it loses money, even if it takes in a lot of money, but all of it goes back out as expenses.