Why? Apple is part of the NSA PRISM program:
While I do think some companies are actively working with the NSA and supplying information to them (looking at you, Microsoft), other companies are "part of the program" only in that the NSA is: 1) storing and siloing communications and records of different companies via their trunk-level data taps, 2) developed a tool to search on this data. It's also possible that covert agents inside companies are providing backdoors, but this would be higher-risk for the NSA if they were directly accessing company servers.
So when a company is added to that list, I believe it's not necessarily that this company is working with the NSA, but that the NSA has developed another "plug-in" for their tool which supports X company's data formats and encryption schemes. As the slide states, the data "varies by provider". This is probably because some companies are lax or bad at security, and some are good. I imagine that though the NSA could theoretically crack individual iMessages, even they do not have the processing power to do so in aggregate.
I think this is the case with Apple, because to work with the NSA would be counter to how they generally deal with customer information. If they were working with the NSA, Touch ID keys would be stored in the cloud. Apple would also have the encryption keys for each iMessage account so that they could hand over to the NSA for easy decrypting. And I just believe, as a culture, that Apple would not play ball with a three-letter agency asking for all their data.