It's asking if I paid over $100 to a tax preparer for 2016. Does that mean when I filed my tax return for 2015 in 2016 because I did have a tax preparer file them for me?

YES, you can deduct the allowable expenses paid in 2016. 

However:

"If you paid more than $100, Turbo Tax will ask a series of questions to see if you may benefit from itemizing your deductions, rather than taking the standard deduction.  If you choose to itemize, you will need to upgrade from the Free version."

 It is referring to tax preparation for the 2015 tax year, and any other tax year that was actually paid for during 2016. 

 The reason it is asking for $100 is due to small amounts will not impact the tax return due to 2% rule in the next paragraph. 

This is also a Miscellaneous Itemized deduction so it has to exceed 2% of your adjusted gross income, before it becomes a deduction and that is why it said the $100 in your case.

It is referring to what was actually paid in 2016.  You report income actually received in 2016 and can deduct the allowable expenses actually paid in 2016.  A credit card is also considered payment when charged to the card.