As a experienced engineer I can tell you, before 1.1.4 patch the flame thrower was such weak nusiance I ignored flames (5sec repair CD on extinguisher) on everything but Baloon and guns.
Being flamed now is certainly more annoying than before, but still nothing like pre yesterday's balance hotfix Banshe and Manticore (not even close to the being in the same league as those two).
As for flamer only being good against greenhorns - not realy. Gatling-Flamer Pyra can still take out Galleons from befind like nobody's buinsess (tested with a great team, including an infamous captain on the galleon).