American Presidents don't actually have to be voted in - There is a succession plan beginning with the VP, though the heads of congress, and into the cabinet (although most of this is academic... I'm not into American History, but I don't think its gone past the VP before).
True, it's never gone past VP. However, we need to know that the presidentail succession plan is a contengency plan, IF the presedent dies or abdicates, THEN the VP is acting President. IF the VP dies or abdicates, THEN one of the cabinent members is acting President, and so on and so forth. It would be near-impossible for the US to actually be leaderless, except for an extremely well-planned assassination team that independently tracks everybody in the succession line and kills them within the hour...
But as for Eden... well, quite frankly, he's a supercomputer inside of Raven Rock, which wasn't inhabited by the Enclave at that time. Rase your hand if you think the Enclave actually held a vote and elected Eden into office... Furthermroe, raise your hand if you think he was actually part of the contegency plan...
In all likelyhood, Eden used the Oil Rig disaster to make his move to power, and has been acting as president and issuing orders ever since. Since the remainder of the Enclave probably didn't know what was going on, they went into the default "follow the chain of command" mode; after all, if some guy has access to high-level comminications frequency, approrpiate proof of authority and whatnot in a post-apocalyptic world, he's probably who he says he is.