It's a reference to the Wug test. Specifically the prompt "This is a man who knows how to gling. He is glinging. Yesterday he ______"
At the time the test was developed, it was commonly believed that children need to be instructed on how to conjugate each individual word they learn, or else they will end up englishing very ungoodly. The test showed that even young children have a grasp on how to pluralize and conjugate even unfamiliar words, and can make guesses on the meaning of new words based on context clues.
Talking in terms of hope or wishing them luck is a good substitute. Serves the same purpose, but doesn't carry the god baggage. It also has the extra benefit of sounding more sincere, since it's just non-standard enough to give the impression that you actually put thought into your well-wishes without sounding seriously unusual.
My go-to is actually variations of "I have faith in you" and then encourage them based on whichever one of their strengths is most applicable. For example: "You're smart. I have faith that you'll spot whatever opportunity presents itself next."
And of course, there is the classic atheist thing of replacing the thoughts and prayers with actual help. A lot of the instances where thoughts and prayers are actually appropriate include times where they need emotional support, which costs nothing but time and energy.