So, I've reevaluated my opinions a bit.
The mode is heavily flawed not necessarily because Nefarian is flat out unbeatable, it's because Nefarian has the possibility of obtaining positions where he cannot lose very early, or just pulling a win out of his ass via the hero power.
There is, as shown multiple times now, the infamous starts involving the 6 mana legendary that reduces all of your card costs by 3. Getting that card early can flat out mean you just win the game on the spot. If you play the cost reduction dragon on turn 1 (with coin) or 2, you've already gotten immense value out of it and there is no way for Ragnaros to kill it that early. He has to wait until 3 mana to play the "deal 6" battlecry minion IF he has it.
Additionally, Nefarian's deck has 2 Dragon Consorts and, coincidentally, a deck chock full of incredibly powerful dragons. It's not unheard of to go, say T1 Dragon Consort, T2 Chromaggus. Good fucking luck beating that after Nefarian has drawn a few bonus cards. Even getting a cheap Chromatic Dragon or Dragonkin Hatcher is extremely strong early.
Presuming the Nefarian didn't flat out win the game from goldfishing with mana reduction shit there is the issue of his hero power. It's just too random. You either get something unusable (deadly poison, totemic might, etc) or a 2 mana flamestrike/mind control/lay on hands/ etc. Even something like a 2 mana Assassinate or Recycle can end up being backbreaking.
It's true that Ragnaros generally has a stronger late-game, but Nefarian effectively draws a card every turn. It is not uncommon for Ragnaros to actually run out of cards before Nefarian despite starting off with less mana and being considered the "control" deck of the matchup. Additionally, as mentioned before, even if the Ragnaros survives the early game and gets his hero power, Nefarian can luck out with a clutch MC or whatever, he can just sweep the rug from under Rag's feet randomly.
In conclusion
Yes, Ragnaros can win, but more often than not Nefarian should win. He has an undoubtedly stronger early game, capable of essentially winning on turn 1/2. Even if Rag survives to his favored lategame, Nefarian can still flip the table with the hero power. Just because you got lucky as Rag facing off against a retarded Euro with a basic cardback who's never touched ranked, or someone with a hand full of deadly poisons and totemic mights doesn't change anything.
This is a 'problem' because there are no options. You cannot construct/modify a deck to counter this. You don't choose whether you want to play as Rag or Nef. You enter the match and have a 50/50 chance to either get the guy who should win ~75% of the time or the guy who should win ~25% of the time.
This would've been way better if they gave us, say, 4 options to choose from. Throw in Kel'Thuzad and Emperor Thurasan or something. Could've made for a really neat metagame where certain raid bosses beat out others, etc. Instead we've got a series of coin flips, and frankly, Hearthstone is enough of a coin flipper to begin with.