First of all, you are right; the tax is on net profit, not revenue. However, the individual owner or owners are taxed on that net profit, not on what they actually withdraw from the company. This means 3% less money to invest to expand the company. So, if a company clears say $1M split between two or three owners, and those owners are trying to grow the company by leaving as much money as they can in it, they have to replace that $30,000 somehow. That means one less job. Add to that the end of the Bush tax cuts, and there goes another job.
Actually, no. There is a $185,000 or thereabouts immediate capital write-off for small businesses, so you can reinvest up to $185,000 and write this off in the current tax year. Only then do you start to have to depreciate your capital investments. Moreover, if you have been investing in your business for the long term, you should already have a lot of recurring depreciation against which you can make new investments.
Anyone who runs a small business already knows this.
And given all the other tax advantages of owning a small business, it is not actually the well-off small businessman (who is the target of this tax) that is getting screwed. It is the salaried workers who get screwed.
Like I said. I am not in favor of raising taxes on anyone. But this particular cult of the sacred small businessman is worshipping another false god.