As I said, Egwene isn't "evil", she's just... Not really all that "nice" or "good" a person, and that tends to rather stand out to a lot of readers because. Well...
Of the main "good guys", and hell most of the minor ones for that matter, she's alone in that respect. A lot of the others do a lot of very not nice things over the course of the books, but with them there's, most of the time, a sense of "they have to do it", with her... More often then not the sense is more "it's more convenient for her".
Of all the characters in the books, and I do mean ALL the characters in the books, the only one who even seems to NOTICE this aspect of her personalty is Rand... And, though it might of played a part in him breaking up with her, he never really seems to give much of a crap about it... Hell, sometimes he even seems to find it funny/endearing.
Mix together a perceived moral failing, with the person in question NEVER, in all of 14 huge books, getting called on said failing... Hell, getting praised for it half the time, and... You've got the makings of a LOT of fan hate.
Still... With all the "observant" people in WoT... How in the bloody Pit of Doom is Rand the ONLY one who seems to ever notice this side of her?
I think that is quite true, though if Rand was in love with her / still loves her as a friend, he may have been somewhat willing to let in slide.
I'm not convinced they considered each other that much of friends by the end though, and indeed Rand seemed to use her nature somewhat to manipulate events at the Fields of Merrilor, up until she proved even more obstinate than he expected.
I think Moiraine may have seen more of her true nature as well, seeing her reactions to Rand in Tear, and then when she started treating Egwene as Aes Sedai / somewhat of an equal, she also started holding more back from Egwene at the same time, suggesting she didn't trust Egwene's likely reactions to certain information.
Cadsuane may have been another one to see Egwene for what she was really like, but never really had the opportunity.
