basically if you've got a squad pouring fire at close range into an enemy unit thats in cover flamers are ideal weapons.
Example: 10 Guardsmen in cover that give them a C.Save of 3+: you get close up with a squad of marines with a flamer (or 2 with Cleanse and Purify).
Now those lovely IG have got the choice between using their cover save to protect against the Bolters (that would normally rip right through them) but that doesn't really protect them as the Flamer ignores cover saves and so will take a great big chunk out of them with no save at all...you can't choose to mix cover saves and normal saves in a squad, everyone takes one or the other
A great combo in theory is using cleanse and purify to get a flamer and plasma gun in the same squad- that way small squads of enemy heavy infantry (Terminators for example) are screwed. They can use their normal save against the flamer but the plasma rips through them, they can choose to use a cover save but the flamer makes a similar mockery, or they could use their paltry invulnerable save of 5+ which even bolters can get past 2/3 of the time...