The reason Gotti wasn't killed was because for one he was always on camera and two he really wasn't on the streets for very long. The people who were after him also had other affairs to attend to within their own Families, killing Gotti wasn't top priority. But had he been on the streets for much longer my best bet was that he would've been killed, it was only a matter of time. The fact that Ruggiero and Gotti weren't killed comes down to sheer luck, not out of any fear they wielded.