Interesting issue.
If as an employee, I was flying on a business trip and through the delay I lost a days productivity on that trip, my company is the one 'inconvenienced' so morally, compensation is probably due to the company.
Where my return was delayed and that delay runs into a weekend, I've no doubt the money is due to me.
Thankfully, we can all sleep with a clear conscience because the legislation states the passenger is due the compensation.