Without explicit cooperation between Apple and the US government, authorities could still be monitoring Apple users. According to The Information, Apple is worried the servers it has been using might be bugged. We already know the NSA intercepts equipment to install backdoors, so this is a legitimate concern.
Combined with a lack of ideal performance from its cloud providers, the security issue has pushed Apple to build an infrastructure only they will maintain.
For a long time, Apple has reportedly believed it's possible the "servers it ordered" had "additional chips and firmware" added to them. The firmware and chips would allow government agencies to spy on Apple and possibly their customers.
Apple has been so worried about shipment interceptions, it's even assigned people to take pictures of incoming servers. Those pictures allow the company to stay on top of all the chips and motherboards being used, making it hard for a government-placed component to slip by.
By "building its own servers with motherboards it designs," Apple can reduce the government's spying ability, says The Information's report.
On top of the snooping problem, Apple also wants to use its own hardware because it's been unhappy with the performance offered by the likes of Amazon and Microsoft. Some Apple services run on Amazon Web Services, Microsoft Azure, and the Google Cloud Platform, but that setup isn't ideal.
Apple claims that Amazon's cloud doesn't load photos and videos onto iOS devices fast enough, according to VentureBeat. Under its "Project McQueen" plan, Apple is constructing its own internal cloud that should offer superior performance.
Due to problems with Amazon Web Services, Apple tried to move to Microsoft Azure. In the short term, that has helped, but Azure is reportedly unable to keep up with Apple's growing demands. With iCloud and iTunes already reliant on multiple cloud providers, there's nowhere else for Apple to turn but inward.
As the old saying goes, "If you want something done right, do it yourself."