I think that Namor is drawn to Doom for the same reasons he's drawn to the X-Men. Namely a sense of empathy and familiarity.
Namor has lived his entire life as one who is considered an outcast and misunderstood, even by his own people and held a heavy burden of one who must care for and shepherd these same.
Personally, I agree this is flawed thinking and can have serious repercussions, especially with his association with Doom. I know Namor is intelligent enough to understand Doom is NOT a good associate. In fact, as I recall, the reason he allied with Doom originally (in the 1970s "Super-Villain Team-Up" series) was due to a chemical imbalance caused by his metabolism and long-term dehydration which, even though Reed had given him the new black suit to help, it still took time to rebalance. However, that obviously can't be the entire issue, because he's re-teamed with Doom on several occasions. Here again, I think it's due primarily to misguided empathy, the same misguided empathy that has teamed him with Tigershark and should make Magneto a likely ally, as well.
This goes a long way to explain why he's often in a category by himself. He's an Anti-hero Which doesn't mean he's against heroes, it actually means he appears to be contrary to what a typical hero is, say if we use Captain America as the standard (Boy Scout, Do-gooder, etc.), Namor is no boy scout, but his goals are usually noble, and very complex. He is generally on the side of good, but can appear to be a villain due to his nature to seek vengeance and a personal sense of Justice at almost any cost.
We have many examples of Namor's own sense of morality, such as when he (justifiably) murdered his own son Kamar, then dressed Kamar up in his own royal garb and trident, and left his rotting bones for Iron Man to find when Namor and the Atlanteans fled Atlantis to hide from Iron Man and surface justice. Iron Man was temporarily deceived, which gave Namor the time necessary to get his people to safety.
I think this is why you and I share a love for Namor... He's complicated and will do what HE thinks is necessary to do RIGHT. He obviously doesn't share traditional Western values or sense of morality, especially not Judeo-Christian Ethics, but he lives by a code of honor and is typically consistent, though in a pinch, he will conform to a group's morality when necessary (Invaders, All-Winners, Avengers, Defenders, X-Men). However, his status as an outcast and a loner most of the time has left him majorly conflicted at times and full of angst, and a sense of carrying the weight of the world on his shoulders.
To be honest, this is also why I like the Silver Surfer... same values and reasons for his actions.
Just my personal opinion.
Torch, flame off.
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