I think that an element of this debate as to whether Shep's pursuit of Jack can be considered manipulative comes down to one of the most well-realized aspects of the character; the fact the audience can really feel how vulnerable and fragile this hard-edged, angry woman really is. As an audience we can see she needs something to transform her existance; it's that or she continues to circle the drain until one day she finally manages to get herself killed. Now based on the majority of responses we've cycled out in here, that transformative force need not be the influence of a lover; some people want to mother Jack, others want to be her friend, others still just want to shake her a few times in the hope they can jar something loose, but I think I can say we're all singing from the same prayerbook when I say no-one thought sex could be the required prescription for what ails Jack.
Ok, it's not
just sex, but an intimate relationship like what we build between Shep and Jack nearly always has a physical aspect. We all know that as our Sheps get closer to Jack, chances are, unless we spurn her, this situation is destined to get horizontal. We get no sister\\mother\\brother\\father\\BFF relationship because of the game dynamic and (arguably) over-streamlining of the dynamics of relationships in the game; with
everyone it's sex or nothin'. So we see Jack, this mournful-eyed monster made up of a stew of anger, wounds and misery, and instead of giving her the kind of help we'd give someone like that in reality, we, well to put an indelicate point on it, we give her the masculine cure-all injection (I know, we don't all interpret the scene at the end as sex, but go with me for now you argumentative swines

). Bam. Nothin' like a Man to fix you up, Jack. Ugh... it's revolting to even think about it that way, but we do; a little or a lot.
And I think that's why the relationship is sometimes read as manipulative; as humans we all see our perfect way to help Jack, the game won't let us just get her to open up over a few drinks and then give her a little cuddle when she starts to let her emotions get the better of her and then assure her we won't turn our backs on her. Instead we get what we get, and for some of us, it's a little bit clumsy in comparison to what we'd really do... and sadly, it's something we can misinterpret as "I'll say this so I can get in her underwear." I'm not saying a romantic relationship
isn't appropriate, because I can imagine that it could be to some people (and I guess if I'm honest it is to me to a degree at least), but we're all familiar with the way some sleazeballs exploit vulnerability in others. Sometimes Meer's delivery of lines just makes it worse. Hell, if you really want to read into it you could say the same thing about the relationships with Tali, Liara, Thane and even Jacob (if you gauge your responses in his conversations, you can't help but read Shep's pursuit of him as being anything but romantic - she just wants to get her ashes hauled). Saying X results in climbing in the Y-shaped box. Liara is naive, Tali is crushin' on ya, so's Jacob, and Thane is as vulnerable as Jack to the right words said the right way... every relationship that culminates in sex can be read very easily as exploitation of another character's vulnerabilites, feelings and experiences.
In the end we're tarring poor ol' Shep with the douchebag brush
I think at least because we want to help Jack on our own terms. Not the ones the game inflexibly gives us.