Depends what you're using it for. If you're just using it to kill a task IF it has "gone rogue" (very few do but it does happen) then there's no problem.
It's when you use it to automatically kill tasks in order to have "free RAM" where the problem comes in. When you do that, it can not only kill things that should still be running (which can lead to instability) but even impair the speed of your experience because something that could've been in RAM already (or at least cached) was killed and has to be completely loaded from scratch again.
This is the basics of why it's better not to use ATK (for Android 2.2+).
Now, if you use a tool to adjust the built-in memory management of Android, it's a different story. Tools like Autokiller Memory Optimizer or the V6 Supercharger script are examples of these and have some benefits (although not a huge monstrous one like some claim).
Neither of these are really needed though as usually Android handles the memory management on its own competently enough ever since Froyo (2.2).
In any case, the use of ATK demonstrates a poor understanding of Android. Such "power users" tend to be those who try to "take control" of their phones but actually made it worse instead. It's too bad these apps exist. Especially bad are the "antivirus" apps which can't actually do anything since the security model in Android doesn't allow them to scan another app.