Okay, I am going to say this RIGHT NOW that I am about to go into a very dark place with my theory about what Ellie is. If you lack the emotional and mental maturity to handle that, I suggest you skip right on by this post.
All the sensitive types gone? Good. Here's my take.
Ellie's world revolves around rape and sexual assault.
Think about it; she's thirteen. The world went to hell twenty years ago. At the time she was born law and order simply did not exist. All we know of her childhood is that she grew up in a military orphanage. No mention is ever made of her father, and her mother is always absent. We are told her mother is a Firefly, so she clearly had some reason to want to fight against the government, such as it is. Being sexually abused by the very people who are supposed to protect her would do that. It also explains why nothing is ever said of Ellie's father. It is implied he is dead at the start of Last of Us, but never outright stated. In Left Behind Ellie has a chance to ask about her mother, but not her father. Why? Because Ellie never knew him - and her mother didn't WANT her to know him.
Moreover, think about Marlene; she claims the only future Ellie has is to be raped and murdered. Isn't that a strange comment from a woman leading the resistance? Maybe... unless you consider that Marlene knows Ellie's mother, and so knows how she was conceived.
And then there's the orphanage again. Lots of children under military guard, with no parents and no-one to turn to but their guards. Do you really think it wouldn't happen? Think about the Left Behind intro again; Ellie has no roommate, and there is no acknowledgement of Riley pointing that out. Instead, she turns the conversation right back to "You're a Firefly now?". No confirmation, nor dismissal. Just flat out avoidance. She also feels the need to sleep with a flick-knife under her pillow. In a secure building, in the middle of a secure compound, she feels the need to keep a weapon with her while she sleeps.
Finally, think about David. His approaches to Ellie have sexual undertones, and look how it ends. The last time Ellie killed someone in a cinematic it was efficient - one shot, one kill. But David? She hits him in the face with a machete in the face TEN TIMES, and when Joel grabs her she screams "Don't fucking touch me!", followed by "he tried to-". She knew what he was going to to do her, and she fought back like a wild animal. That panic suggests she has been through it before.
So where does this all leave Ellie, Riley and the kiss? Because what happened to Ellie is likely not just a rape-and-forget affair; she was probably groomed. That suggests some degree of mental programming, telling her things like "you should enjoy sex", or "I'm doing it to show you how much I care about you." This would then apply to Ellie's other social interactions, and so when she feels a strong bond with Riley she has become conditioned to expect a sexual encounter.
Yeah... suffice to say, I spend a lot of time while playing The Last of Us feeling like I should not be enjoying the game...