Basically, working at home is not in any way good for the company, and it's usually not good for the employee at all, so most companies won't let you do it.
Modded to 5 completely without citation and from what I assume is mostly conjecture. Nice job.
1) Most people are not most productive at home. In fact, most people are significantly less productive at home due to many more distractions around them.
I have seen this first hand. IBM came into our company, hired all of us and then sent everyone home to telecommute. About 1/3 of the people could not cope and got fired; Your statement seems to imply that people are inherently incapable of working remotely, which is complete crap. It's a learned behaviour. The other 2/3 of my colleagues and I went on to have lengthy productive tenures at IBM (without seeing an office or each other for up to 6-10 years at a time).
2) Commuting (at least relatively short commutes) has been shown to be a good way of clearing your brain, and getting it into or out of work mode. It doesn't really hurt productivity unless you're doing it for hours.
Citation please? I'll settle for an anecdote.
While this may be a way of "clearing your brain", "getting into the zone", or whatever you call it: It's a learned routine that tells your brain "it's time for work". You do this when working remotely as well. You get a routine in place that get's your mind ready for work (even when you work at home, it's very important).
3) Skype does not make communication with coworkers a snap. It imparts a major cognitive overhead.
Cognitive overhead? If operating Skype is too difficult or a cognitive overhead for you, then yes you will need to remain on-site to flip the burgers and operate the fryer.
While I personally don't like Skype I feel that a telephone call is just as effective as an in person meeting (except I can't punch someone in the face... I'll let you decide if that's a positive or negative).
4) Communication does not just come down to a few meetings a week that could (with more effort) be done via Skype. By working at home you remove any chance of corridor conversations, which typically, are by far the most productive communication in an office.
Again I'm going to have to ask for a study that says "corridor conversations" are more productive.
How many of you attend 15 minute meetings that regularly sprawl into an hour?
"Corridor conversations" happen all the time when you work remote: Believe it or not working remotely I've been able to establish close personal relationships with people I've never met in person, yet talk to on a daily basis (just shoot the shit for a couple minutes before or after a meeting).
The fact is trucking people and resources to a central point for a few hours a day only to then have a mass exodus in the evening is not sustainable. There are more drivers getting on the roads than getting off. We can't build lanes in big cities fast enough. People are going to have to go home.
I know that in my field (Software/Systems Engineering) people aren't all that social in the first place (everyone has their headphones on all day). Nothing I do requires me, my peers or our management to be located in any specific place. All of the tools required to do my job fit in a backpack and can be easily afforded by me if required.
I've been on-site the last 5 years (after a 12 year stretch remotely) and the co-workers I talk to are fairly miserable having to commute and then sit around in a sterile office environment. I see so many people that think because they show up to warm a chair everyday yet fail to produce anything meaningful they can hold a job (and they're mostly correct). When you telecommute the employer usually has strict expectations you need to meet (it's sink or swim).
The only people I know that really push for the 'on site' mentality in my field are the upper management or shareholders that just want to see their minions slaving feverishly beneath them.
The basic fact is that if you work remotely or commute to work on-site, both are a learned behaviours that require discipline.
Just my 2 cents.