Sure seemed that way to me. Not played up to the extent it could've been, of course. But throughout Halo 4 she repeatedly seems to demonstrate a different sort of affection for John than she had in the prior games. If not outright romantic treatment, certainly more tender/contemplative and less the sarcastic but loyal friend she seemed to be in CE-3.
The moment it really went over the line for me was when she and John are "saying goodbye" in the Composer Nexus thing. I literally audibly groaned the first time I played Halo 4 and she said "You have no idea how long I've wanted to do that," when she touched his chest. I'm not going to be obstinate beyond reason; this doesn't have to be read in a romantic way. It certainly seemed like the least obscure way to understand it to me, though.
I just never thought of John and Cortana as being romantically connected. In the original games, there is a very consistently familiar, friendly and even at times mock-flirtatious rapport between them, as though they know each other extremely well and are very comfortable together. I just always took that closeness to be more of a cop partnership than a romantic relationship. I don't think John would really know what to do in a romantic relationship, even if he deliberately eschewed his militant duty to participate in one (I can't see him choosing to do that, either). As for Cortana, it's established in the Fall of Reach that she thinks John is handsome/attractive, but I don't recall that aspect being explored any further in the gap between that and Halo 4.
It just threw me for a loop how much more of a romantic tone I picked up between her and John in Halo 4. It felt abrupt and quite different than their relationship as I'd understood it up until that point, and it was one of the factors that lessened my immersion in that campaign.