I've gotten pretty good with the flamethrower, I think. It's equally effective at taking down goons as a prifle (unless they run away in an area that they can actually get away... plenty of those areas are around, of course) but has the added advantage of frying dretches that come into the fight as well, without too much difficulty. It doesn't work well against good maras or tyrants though (the former often makes you do more damage to yourself, the latter can just absorb the flame while killing you).
In terms of tk's, just play smarter. Yes, noobs will be noobs and fry their teammates/buildings but it's not just because they're holding a flamer (all that does is make them more efficient). It's similar to using a luci in a group, it just takes practice to learn when and where to shoot.
Finally, even though most people know this, you have to move toward your intended victim for it to work -- not away from them. Also, don't use it if you're aiming at a close obstruction such as a wall, door, etc.
Don't forget to dance!
