Secret Communication Channels Are for Hiding Stuff.
There is no other possible reason for them to exist. For Jared Kushner to have tried to set up such a channel with the Russians means simply that he had stuff he wanted to communicate that he didn't want to be known. Since he's a tool of the Trump administration, one can assume that those channels would have been used to hide stuff Trump didn't want to be known as well.
Syria? Possibly. But such a channel is a means of secretly discussing all sorts of things that would be either embarrassing or outright illegal if discovered.
It appears that no such channel was actually set up, although that may also be incorrect. But the fact remains that an attempt was made to create a means of communicating secretly with a country that has long been an adversary.
We must not forget why such a channel might be needed by the Trump administration. There is no reason for such a thing that is not nefarious in nature, actually.