Wikipedia says that Open Whisper Systems has received a significant amount of funding [1] from the Open Technology Fund, run by Radio Free Asia [2], a US-government-run propaganda organization.
Of course, this is the arm of the US government that very actively doesn't want back doors, because they operate in territories controlled by other not-necessarily-friendly governments. They need communications to be reliably secret, and they have no need to tap those communications. It's the same reason that government funding for Tor isn't inherently a problem for Tor's security, and you see other parts of the US government, like the FBI, trying to hack it.
It's definitely worth worrying that the government could decide that this part of its mission is no longer worth funding. But it isn't likely to be a risk of back doors. (Especially compared to all the other usual risks, notably simple bugs like Heartbleed and Weak DH.)
Of course, this is the arm of the US government that very actively doesn't want back doors, because they operate in territories controlled by other not-necessarily-friendly governments. They need communications to be reliably secret, and they have no need to tap those communications. It's the same reason that government funding for Tor isn't inherently a problem for Tor's security, and you see other parts of the US government, like the FBI, trying to hack it.
It's definitely worth worrying that the government could decide that this part of its mission is no longer worth funding. But it isn't likely to be a risk of back doors. (Especially compared to all the other usual risks, notably simple bugs like Heartbleed and Weak DH.)
[1] https://en.wikipedia.org/wiki/Open_Whisper_Systems#Funding
[2] https://en.wikipedia.org/wiki/Radio_Free_Asia