I've been confused by this in the past as well - the line 17 amount was more than the sum of my withheld taxes on W-2s and 1099s. For me, the answer was "Additional Medicare Tax" from Form 8959, line 24. Basically, if you get charged the Additional Medicare Tax (on top of the core 1.45%), that additional amount (8959, line 24) is to added to your tax paid (line 17 on 1040).
