You will need to specifically identify your military pension so that TurboTax can treat it differently from other pension amounts
Note that other pensions are allowed a $10,000 exclusion subject to modification by Social Security, etc. But, as you say, starting in 2016, military retirement pay is completely exempt from Maine income tax.
First, go to the state interview for Maine. Go through the interview until you see a screen entitled "Retirement Income and Contributions" (see first screenshot). Check "yes" for the first questions (see screenshot).
When you hit Continue, you will see a new screen entitled "Pension Income Deduction" (see second screenshot). Enter your pension amounts here. In the screenshot below, I put $20,000 as the complete military pension.
This will remove your entire military pension from Maine taxable income.