Board Thread:General Discussion/@comment-27620479-20160914150718/@comment-27620479-20160915060854

If you keep fighting Asgore after completing a no-kill neutral run, you get extra dialogue from Flowey. When it becomes obvious that you keep coming back just to see what he has to say, he asks if you want to start the Flowey Fan Club, and then tells you that Papyrus have already done that. The next time you get to know how things worked out between Flowey and Sans before you came:

"If I have ONE piece of advice for you... DON'T. Let his brother. Find out ANYTHING about you. He'll... well... Let's just say. He's caused me more than my fair share of resets. Stay away from that guy."

This is why I guess that Flowey keeps his existence a secret, which is supported by the fact that Sans doesn't seem to know about him.