From your link: The genetic fallacy is a fallacy of irrelevance where a conclusion is suggested based solely on something or someone's origin rather than its current meaning or context.
Notice how it says solely? There's no solely about this. To consider a root is not to ignore current meaning; one can do both. That's, uh, what dictionaries do.
http://www.fallacyfiles.org/afonedis.html
There's another point. The genetic fallacy refers to historical origin. The root of a word is certainly that, but it's also a piece (the main piece, in fact) of the word as it is now. If your point were correct, then a botanist examining the roots of a plant would also be committing the genetic fallacy. Happily for botanists and etymologists, the genetic fallacy applies to one sense of "root" but not the other.
What this means, of course, is that anyone who exhibits even a shred of self-confidence will probably be accused, by someone somewhere, of being arrogant. The symptoms are largely the same. The difference is one of degree, and of results.
Arrogance is hard to diagnose without the benefit of hindsight. It is now evident that Marc Andreesen was being arrogant when he proclaimed that Netscape would kill the Microsoft desktop. But Linus Torvalds was apparently not being arrogant when he claimed that he could build a better VC system than CVS in less than a month, because... he did.
I don't understand people who say success justifies arrogance (or worse, makes it not-arrogance altogether). Success just shields you from the consequences of your arrogance.
Yes, but whose attitude? That of the "arrogant" person, or that of the person who interprets a certain set of actions and statements as "arrogance"?
The problem is that there's only one (e.g.) Linus Torvalds, but he has thirty thousand critics, of all shapes and sizes and cultures, with a widely varying range of personalities. Some of his critics are bound to have no sense of humor. Some of them are bound to have a tin ear for dialogue. Some of them are bound to be jealous as hell. Some of them are enemies. Some of them are trolls.
Successful douchebags (by whoever's standards) are still douchebags.
Someone is labeled arrogant when they're successful enough that others have to pay attention to them, yet those same people are jealous it's not the other way around.
IMHO, the difference is in attitude. Self-confidence says "I'm OK, I'm pretty good." Arrogance says that, plus "oh, and other people suck."
Also, being pretty good implies being better than others. Whether you praise yourself or dis others, you're still saying you're at a high percentile. Being good or sucky is relative.
I do not think 37signals or Jobs is blinded by their confidence. Though one could easily claim Jobs confidence led to his downfall in 1987. He even explained this at the commencement speech at Stanford (I think).
Then, a lot of people are selfish. If you are doing something they don't like, they'll say you're bad, and if you help them out, they'll say you're good.
My (probably inaccurate) conclusion is the people you piss off will say you're arrogant, and the people that you helped out will say you're self-confident.
Nota bene: this is all pretty tentative. My guesses don't represent my opinions, or those of any startups I start in the future.