Matrix was originally funded by AMDOCS, an Israeli communications company that is implicated in using "intelligence gathered from backdoors in Israeli wiretap systems sold to the U.S government to prevent US intelligence and law enforcement agencies from tracking and stopping suspects behind the 911 terrorist attacks." ^[1]

Here is the Fox News four part series on Amdocs’ implication in the 911 terrorist attacks.

It is also known that several founding Matrix developers are current or former Amdocs employees, and Amdocs is known to employ many former (or current) Israeli Unit 8200 agents, Israel Defense Force's SIGINT unit.

From Wikipedia on Unit 8200:

Military publications include references to Unit 8200 as the Central Collection Unit of the Intelligence Corps, and it is sometimes referred to as Israeli SIGINT National Unit (ISNU)

I'll never trust the Matrix protocol, it's developers (whom I've had the unpleasant experience of dealing with in the past), and least of all Matt Hodgson. I urge users to read his dialogue with critics scattered around github and various blogs to get a feel for his ideologies and the talking points he uses.

A reminder that bug-bounty hunters can be bought and paid for, so don't be fooled thinking "open source" means safe or secure. But if you feel you can 100% trust Matrix or don't care one way or another, I say go for it - it's a pretty nice communications package that's easy to install and works quite well. Hodgson is a bit of a tool though.

An interesting side note - Matrix is used for secure communications of Germany's national health care system and by Bundeswehr (Germany's armed forces) to pass classified intelligence. That's...convenient.