depends on what kind of tech you are. Typically beginning techs or "general service techs" are paid hourly. Junior techs are sometimes paid salary, but usually they get the same as the full blown techs which is flag hours. Flag hours are great if you are a good and fast tech, for example; The front end rebuild on my old s10 blazer I had flagged 6 hours total with everything we were doing, my dad (with little help from me as he is much faster than myself) finished it in less than 3 hours. On average my dad earns 60+ flag hours in a 40-50 hour work week. If a tranny swap flags 4 hours on the national average then he gets paid for 4 hours, if he's slow or is working with a tranny he knows nothing about and it takes 8 hours he still only gets paid 4 hours, however, if he is working on a tranny he knows and has worked on before such as the common 700r4 and finishes it in 2 hours he still gets paid the full 4 hours.
Good + Fast = great pay
Slow = not so great pay
So if you're not fast and experienced flag hours can be a bad thing. If you are fast and experienced then flag hours are a blessing.