1) in some industries (like in finance) the regulatory requirements make it near impossible to use external email services. For example, there needs to be a record of every email sent out of accounts in the company that needs to be presented to regulators when they demand it.
2) People within the same company may slip up and send emails to coworkers that shouldn't be read outside the company. When you run the email servers, no other party reads them. It stays in the family, so to speak. When you use google or whatever service, they get a peek at the emails.
3) AFAICT Gmail is not HIPAA compliant, making it inappropriate for health care businesses.
Or to put it another way... we're a 2 person, self-funded, bootstrapped startup. Our most precious resource right now is the time of myself and my cofounder. Every minute we spend tweaking and tuning an email server, is a minute we're not talking to customers, doing market research, working on our product, developing strategy, doing competitive intelligence research, etc. For us, that's not a tradeoff that makes sense.
That and then there are periods throughout my day (especially at the $DAYJOB, like right now) when there isn't anything productive I can really do on the startup, and there aren't any pressing assignments, so reading HN is about as productive as anything else. :-)