Curious why you feel that way? I see it the other way.
To quote a great philosopher, "You want it to be one way, but it's the other way."
Cruz likely would've won this time around if not for the Trumphenomenon. All these people voting for Trump in the primary aren't just going to say "Ahh well our guy lost, let's just go back to what the establishment is feeding us, Paul Ryan!"
You hear the samething with Kasich "oh people like Kasich, oh he's the adult in the room, he has broad appeal." Dude is getting like 10% of the vote. I mean he is being soundly rejected by the people in these primaries.
The fact of the matter is that for whatever reason, right now people are voting for anti-establishment, ideologically extreme candidates. If there is 4 years of Hillary Clinton, what would really change? If anything these people would just feel more emboldened and validated that a major disruption is needed. Trump and Cruz have a lot of differences, but many of their voters aren't voting for establishment candidates for the foreseeable future I don't think.
Then you factor in stuff like ground game already in place, early primary terrain which is Southern states and it starts to look pretty good for Cruz.
I say all this assuming it is Trump v Hillary and Trump loses. If Cruz were to lose to Hillary then obviously it might be tougher for him in 2020.
This is also a reason someone like Marco Rubio shouldn't formally endorse Cruz, because he might have to explain that on a debate stage in 4 years.