There's a distinction between trusting a company not to look at your data when you hand it to them in plaintext, (Skype) and trusting them to have completely flawless, bugfree code that the NSA hasn't backdoored. (Dual_EC_DRBG)
I'm not sure what parts you can verify, but I'm willing to trust the word of those at Whisper. Perhaps I'm naive but they seem to genuinely care about improving privacy for others.
This comment also shows that privacy is always based on trust. Trusting Cisco, Google, Microsoft, OpenSSL devs, Whisper Systems, whatever. You can decide who's more sympathetic, moxie, Zuckerberg, Nadella..
That was exactly the point I was trying to make when I responded to someone saying "well, with E2E encryption you don't have to trust them". Yes you do.
