They can if they want Google services.
There may have been concern from banking apps and the likes as well? Though it's been a while since I've looked it up.
Edit:
The Strategy
In general, it is difficult to balance the needs of the average user who benefits from Android’s built-in security mechanisms and the user who wants more freedom. Companies like Google and application developers expect their code to run on a trustworthy device and will only provide their services on such devices.
Fairphone has made the conscious choice not to offer an option to root the device on its Google-services enabled software.