On the Qualified Div & Capital Gain Tax worksheet, why are qualified dividends (line 2) subtracted from tax. inc. (line 1) when they weren't included in TI to start with?

sure they were included in taxable income.  they are included in total dividends reported in box 3b qualified dividends are just a subset of total dividends

To arrive at the line 7 amount, which will be used later on the work sheet.

The line 7 amount is taxable income with qualified dividends (QD) (and Long term capital gains, if any) backed out. It identifies the amount to be taxed at ordinary income rates.  

The QD is included in taxable income ( TI). It  needs to be backed out, so it can be taxed at long term capital gain rates.