I'm a big fan of flexible working hours. I'm one of the few that gets in early and leaves early due to family commitments. I do seem to be in the minority as most techies seem to prefer to come in late and leave late. I also don't have to stress about being late, because my employer knows that I'll make up those hours.
One problem I've discovered being an early starter is around crunch times. I've found that there's an there's an implicit pressure and bias by the team to have everyone working late until the same time. This isn't so much of a problem for late starters, but for early starters they may have already put in 2 to 3 hours of work before others arrive.
All I ask for is teams with flexible working schedules accept that around crunch times early starters might stay late, but not as late as their later starting colleagues.