It's certainly not free to run and maybe it doesn't really make sense for Microsoft to run Outlook.com anymore, except that it's an easy way to motivate people to having a Microsoft account.
Outlook.com certainly has to show up as an expense, one that Microsoft would like to reduce. When you look at what other providers charge for a single email account, it's hard to see Microsoft making money of Outlook.com. There's obviously something to be said for scale, but still, it must cost them something.