Tony's motivations by the end of the series

Think about it.

Tony personally kills Febby Petrulio, but then again he acts alone.
Paulie and Christopher carry out the hit on Mikey Palmice. And they later try to kill the Russian who gets away.
Gigi carries out the hit on Philly Parisi, though Gigi himself later dies from trying to take a dump!
Tony and Pussy kill Matt Bevilacqua.
But Pussy is himself later killed by Tony, Sil, and Paulie.
Janice kills Richie but since she is otherwise not involved in the mafia's affairs there is little chance of her getting busted for anything major.
Ralph kills Tracee and later orders the hit on Jackie Jr, which is carried out by Vito. But Ralph is later himself killed by Tony and Vito is later killed by Phil and his men.
Bobby's father carried out a hit in season 3 only to die literally a few minutes later from crashing his car thanks to a coughing fit.
In season 5, Tony, Christopher, and Tony B all exhume some bodies from Uncle Pat's farm before they can be discovered. But Pat is retired and if he was going to become a rat, it would have happened already. He is thus as harmless as Janice in that way.
Tony later kills Tony B and Christopher.
Carlo and Sil kill Fat Dom for killing Vito but Carlo become a snitch by the finale--if I understand everything right--so that cat is out of the bag.

Furio helped Christopher dispose of Richie's body but he goes back to Italy at the end of season 4. Maybe Tony tried to have him whacked. Or maybe he didn't bother.
Christopher probably had someone help him dispose of Tony B's body but we don't know who and he probably never told Tony.

That leaves Tony, Sil, and Paulie left by the end. Sil is in a coma and Tony seemed like he was considering whacking Paulie when the two of them went down to Florida after the first guy they killed together was found.

There were examples of Tony using "layers" to protect himself from being linked to murders.

For the Rusty hit, Tony ordered Chris, Chris went to his junkie friend, the junkie contacted the Italian guys, who did the job and immediately got on a plane back to Italy.

Junior also protected himself when he ordered the hit on Tony. He told Mikey, who went to the guy who he later killed, and that guy got the two guys who attempted to kill Tony.

Most of the time, they were just a smaller family, so it was harder for them to put extra layers between themselves and murders. Other times, the hits were more personal for them, like with Big Pussy or Tony B.

Yea, its a plot hole within the series