There's no neat way to bend the rules just for Flare - you need specific card text on either Counterspell (e.g. "Does not counter Flare") or Flare (e.g. "Immune to Counterspell") to make that happen, which is very inelegant.
Also, it's fair since Flare is only a 2-mana card while Counterspell is a 3-mana card. If you use Flare to trigger Counterspell, you are actually ahead tempo-wise and can safely use other more valuable spells.
So yes, I think Counterspell should counter Flare too.
If you think that flare should still get its effect when counterspell is in play, do you also think other spells should get their effects while counterspell is in play? For example, should deadlyshot kill an enemy before counterspell is triggered? Spells should be treated the same regardless of effect after all, it's not yugioh where you have different spell speeds.
Personally, I feel like Flare should destroy Counterspell, purely based on the flavor and feel of the card. However, if it did work this way, as others have pointed out, it wouldn't make sense based on Counterspell's text and the mechanics of the game. There's no good way to redesign the cards so that Flare does destroy Counterspell, so I guess we just have to put up with the sadness of our Flares being countered. Or use Eater of Secrets in wild.
flare should read "destroy most enemy secrets" then. How else are you supposed to play around 2+ Ice blocks depending on mages random spell? And don't say eater of secrets. Its bad in constructed and most arena games.