1. Per a character style: use Strikeout (and use the Strikeout Options to move it into position). This is easy, but the strikeout is slightly wider than the underlying character. It also needs proper positioning per each font size -- the distance is absolute. (Note To Adobe: plz add!)
2. Per Glyphs: find a non-spacing macron in your glyphs. "Non-spacing" means it automatically gets offset to the left, so it positions roughly on top of your base character. If your font doesn't have a non-spacing macron (not sure about Times New Roman), use the spacing one and adjust the position using manual kerning.
3. Per IndyFont: Create a One-Character-Font (http://www.indiscripts.com/post/2012/06/indyfont-build-opentype-fonts-from-within-indesign). You can either build just the non-spacing macron, or, if you only need it on top of a single character, draw it in-place.