(Just to save everyone some time, here are the relevant quotes.)

HPMoR Chapter 61, Dumbledore to McGonagall and Snape:

His strongest road to life is the Philosopher's Stone, which Flamel assures me that not even Voldemort could create on his own; by that road he would rise greater and more terrible than ever before. I would not have thought Voldemort able to resist the temptation of the Stone, still less because such an obvious trap is a challenge to his wit. But his second avenue is nearly as strong: The flesh of his servant, willingly given; the blood of his foe, forcibly taken; and the bone of his ancestor, unknowingly bequeathed. Voldemort [...] would certainly seek the most powerful combination: the flesh of Bellatrix Black, the blood of Harry Potter, and the bone of his father. Voldemort's final avenue is to seduce a victim and drain the life from them over a long period; in which case Voldemort would be weak compared to his former power.

Dumbledore, at least, thinks the obviousness of the trap won't preclude its success.

HPMoR Chapter 76, Quirrell to Snape:

A single glance would tell any competent wizard that the Headmaster has laced that corridor with a ridiculous quantity of wards and webs, triggers and tripsigns. And more: there are Charms laid there of ancient power, magical constructs of which I have heard not even rumors, techniques that must have been disgorged from the hoarded lore of Flamel himself. Even He-Who-Must-Not-Be-Named would have had trouble passing those without notice.

That second bit is particularly interesting. It seems to suggest that Flamel would have been capable of protecting the Stone himself just as well as it's being protected now, in which case why have it at Gringotts in the first place?

The question in my mind is: how could Voldemort know if the Stone in Hogwarts is fake or not? I mean, the situation seems to be that Dumbledore went to visit his old teacher Nicholas and came back with a "Philosopher's Stone" in a small leather bag, which he deposited at Gringotts, and later took to Hogwarts. If you assume he actually is trying to protect the Stone, it would pretty much have to be a fake, wouldn't it? (It'd be pretty funny if the real one was teleported into the Marianas Trench or something.)

And I think it's something of a mistake to assume the only reason for breaking Bellatrix out of Azkaban is the resurrection ritual. Suppose that he does already have the Stone - maybe he replaced it with a fake months ago, maybe he invented it on his own, whatever - wouldn't it still be useful to him to retrieve his most powerful and loyal servant?