The decision to hide the Potters was done partly on the basis of the information that Snape passed to Dumbledore after he'd overheard Sybill Trelawney's prophecy.
"Hide them all, then," he croaked. "Keep her - them - safe. Please."
(Deathly Hallows, Chapter 33, The Prince's Tale).
Later Snape makes Dumbeldore promise that he will never reveal his true feelings for Lily.
There was a long pause, and slowly Snape regained control of himself, mastered his own breathing. At last he said, "Very well. Very well. But never - never tell, Dumbledore! This must be between us! Swear it! I cannot bear...especially Potter's son...I want your word!"
"My word, Severus, that I shall not reveal the best of you?" Dumbledore sighed, looking down into Snape's ferocious, anguished face. "If you insist..."
(Deathly Hallows, Chapter 33, The Prince's Tale).
However, that conversation happened after Lily was already dead. Do we have any way of knowing whether or not Lily knew the real reason why she and her family were to suddenly go into hiding? Was she told that the Fidelius Charm was being cast on the basis of Snape's information? Or did she go to her grave entirely unaware of Snape's continuing feelings for her and of Snape's true loyalties?