Well I've interpreted the rules (thematically) in the opposite way to Dakuth - and I still do.
<rule>If all the resources are blue, then the Sympathizer card effectively becomes a 'You Are A Cylon' card, the player moves to the Resurrection Ship, behaves as a Cylon player with noted restrictions.
<my opinion>The card being treated as though it reads 'You Are A Cylon', combined with the fact that you immediately move to the Resurrection Ship, as far I'm concered, makes it clear that, in this situation, the Sympathizer is a Cylon. Why would a Human suddenly move straight to the Resurrection Ship, rather than, say, the Cylon Fleet in general? Whereas, a Cylon who was on Galactica and was discovered as a Cylon (sympathetic or otherwise) might be executed and thus end up on the Resurrection Ship. I see it as the reason they don't get a Super Crisis card is that they sympathize with the Humans, so don't want to bring down a Super Crisis upon them. They don't get to control the fleet, because the other Cylons don't trust them enough as they've noted that this character is sympathetic towards the Humans.
<rule> If one resource is in the red, then the sympathizer card is effectively a 'You Are Not A Cylon' card, the player moves to the brig. That's it.
<my opinion> Again, the card becomes a 'You Are Not A Cylon' card and you're simply stuck in the brig. The key for me is that, as mentioned, the card becomes a 'You Are Not A Cylon' card. In addition, thematically, a Cylon wouldn't be simply put in the brig and then let out later to wander around the fleet etc (I may be wrong, it's been a while since I watched the series).
However, it's all semantics, really as the rules state that All Cylons win together and all Humans win together so, unless the Sympathizer who's card becomes 'You Are Not A Cylon' also has another card that states 'You Are a Cylon' (as one 'Are' card overrides all 'Are Not' cards), then according to the base rules the sympathizer who goes to the brig is a Human and the one who goes to the Resurrection Ship is a Cylon.
(Yes, I'm aware there's only one sympathizer)
The way I've interpreted the thematic meaning of the rules does, however, then support variants where the Sympathizer who goes to the brig wins with the Cylons and the one who goes to the Resurrection ship wins with the Humans.
I don't know what current variants exist, but the way I see it mechanics wouldn't really need to change at all to have the Sympathizer win with the opposite team. I mean, the action on the 'Human Fleet' location does say 'Look at any players hand' so could be used to steal cards from Cylons.
After the Sympathizer breaks out of the brig he/she can still send other players there to limit the Humans' capabilites(might be hard, but even revealed Cylons at the Cylon Locations still contribute to skill checks and you can at least force other players to waste cards trying to stop you), same with assigning the presidency to someone you think or know is an unrevealed Cylon. You could use 'Communications' to move civilian ships into danger or 'Command' to move Vipers away from Cylon ships or pilot one yourself to take control away from the Humans. Imagine if the last Viper was launched and Sympathizer Apollo just jumps straight in it!
In short - the 'Are Not' Sympathizer (who goes to the brig) can behave just like an un-revealed Cylon, but can be completely blatant about it as there's no fear of being found out (hand and card secrecy should still apply). Yeah, you could keep getting sent to the brig, but they'll have to waste cards to keep you there. If the Cylons win, you win.
The 'Are' Sympathizer (who gets sent to the resurrection ship) messes with the Cylon's plans by stealing their already limited supply of Skill Cards. Even the 'Caprica' action lets you get rid of the more harmful crises. If the Humans win, you win.
Completely changes the dynamics of the Sympathizer game with... actually no changes to the game rules whatsoever, other than who the Sympathizer wins with.