People take a lot of time off when they work from home. I am as guilty of this as anyone. People tend to focus more on work while they are in an office. Also, it is much easier for managers to organize the work when the people being organized are within line-of-site. The pattern I've seen emerge at New York City startups is:

1. the leadership and most important employees meet at the office 3 to 4 days a week.

2. less important employees are allowed to work from home

The workers in group 2 are in direct competition with outsourcing firms in India, Vietnam, Brazil, etc. If you are just an average frontend programmer, and allowed to work from home, there is a good chance that your work can be sent overseas. So workers in this group are seeing more downward pressure on their wages, and have a more precarious position.