Let someone bring anything near the evidence of A-Rod's use that we have of Bonds' use, and the questions are legit. I think given what happened to baseball with drugs entering the game, ANY question of ANY player is legit. Performance-enhancing drugs are clearly a part of the game. And these are just questions--natural questions given the environment in the sport. It should be an easy "yes, I did it," or "no, I didn't," answer.
It would be patently unfair, though, to just assume A-Rod used. It's not like there are doping schedules, a shady personal trainer who was a known supplier who is sitting in jail because is protecting A-Rod, a shady drug dealer who was supplying drugs to dozens of athletes, and A-Rods name popped up all over his files, A-Rod doing ads for body building magazines for him, etc. There isn't the grand jury testimony of A-Rod in which he fumphers around and states the ridiculous. And there haven't been the kinds of physical changes in A-Rod that make use a no-brainer for anyone with eyes. He bulked up last year (also slimmed down this year), but it was nothing like Bonds in 1999 when he showed up at spring training and teammates were like, "WTF?" and calling him the Incredible Hulk (Bonds has only gotten bigger since then, particularly after Greg Anderson hooked up with Victor Conte). Plus, A-Rod has pretty much hit the tar out of the ball since he was in his teens, with a skinny, but athletic body. It isn't like he had one career and then after the age of 35, he had a second super-human career.
Did A-Rod use? Who knows. My guess would be no (and I could be WAY wrong). But Chipper Jones is way off. Barry Bonds being under a cloud of suspicion ISN'T just a product of his breaking the record. There is ridiculous evidence that he used and that it had a pronounced effect on his performance in his late 30s and early 40s. So he wouldn't own the record without that use. Show any amount of similar, compelling evidence that paints such a complete picture of use related to A-Rod, and then maybe Jones has a right to spout off about him.
But no, they are not the same thing, not given what we know today.