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The writer agrees that most small business owners have incomes < 200 or 250K. Then in the next sentence he says that most small business profits will be taxed at the higher rates.

Most small businesses earn little or no profit (or operate at a loss). The small percentage (2-3%)of small businesses that have incomes pushing their owners into the over 200 or 250k level earn over 50% of the profits. He's talking about two different percentages. In the first, he is discussing percentage of total businesses. In the second, he is discussing percentage of total dollars profit.