The reason is trivial - if you are not around half of the time rest of the team is, teamwork suffers quite a bit (which is cca constant situation with distant remote places like India, ie if you have any questions in the afternoon you are blocked and they need to wait till next day)
Those aren't the only companies that exist.
No significant numbers of people - in Zurich at least - are starting work in offices at 6am.
The vast majority of useful work I ever did was between the hours of 6-9am.
I agree with your sentiment but I think in this case, it's misplaced.
I do 6:30am - 3pm and have done for years, it fits my day well. Others I work with might not start till 10am. Thats the great thing about working from home, you get more flexability in your start/end time. As long as you get your working hours done it's a total non issue.
Personally I appreciated the flexibility to work and leave early.