The show tells straight us that Abigail cares for Will.
“Last thing before casting a line: you name the bait on your hook after somebody you cherished.”
"To say goodbye?"
"If the person you named it after cherished you, as the saying goes, you will catch the fish."
"And what did you name it?"
He caught the damn fish, therefore under the symbolic logic of the narrative, she must have cherished him.
However, what you’re looking for is evidence specifically from S1 that each cared for the other. I held onto this post for so long because I was certain I had answered it before, but I couldn’t find it in my “Abigail Hobbs” tag.
But I did just find it! (I had a typo in her name, argh.) So here it is, but I’ll quote here the relevant part of the discussion.
Abigail got deeply involved with Will and Hannibal because they simultaneously orphaned her and saved her life: Hannibal through the phone call and the first aid, and Will through shooting her father before he could cut her throat cleanly.
She bonds more closely to Hannibal partly because he makes an effort in a way Will does not because Will has concerns about being inappropriate in a way Hannibal does not, such as when Will elected not to give Abigail the magnifying glass and fly-tying gear. He did not want to dig up memories of her father teaching her how to hunt. But in the same episode, Hannibal serves Abigail sausage and eggs exactly because that was the last meal that her father was making on the day Will shot and killed him. Their shared secrets, the meal and psychedelics, Hannibal’s physical warmth and presence: these were all things that helped Abigail bond to her new captor. “You bond with your captor: you survive. You don’t: you’re breakfast.”
By comparison, Abigail had much more mixed feelings about Will. She’s not comfortable with him the way she is with Hannibal, but she looks to him to help her understand her father and what happened to her. She asks him what it feels like to kill someone, and she trusts and uses his words as her gauge after she herself kills somebody. She asks him what it felt like to be her dad, and looks to him for reassurance about being messed up and having nightmares. We know she’s taken to Will because she wants to emulate him: when Hannibal asks her what she would like to do with her life, she tells him that she would like to become an FBI agent. When Will doesn’t see her for a few weeks, she complains to Freddie that he’s avoiding her. She doesn’t hesitate to go with him to Minnesota to try to catch the copycat, and when there, she steers the conversation so that she can finally unburden herself about being her father’s lure to him in the same way she had unburdened herself to Hannibal.
If nothing else, this desire to be seen and known by both Hannibal and Will is evidence enough of her attachment to each of them: this is the language of love on Hannibal.
Will frightens her because of his similarities to her dad, his own brand of weirdness, his encephalitis, and the fact that others, particularly Freddie Lounds, are constantly telling her that he’s a killer. He’s “stained” to her because he killed her dad. But she still cares for him, especially after she discovers that it wasn’t he, but Hannibal, who killed Marissa. But she’s in deep at that point, and as she says, she doesn’t know what else to do, so she just does what Hannibal told her.
There’s also this further comment by platoapproved, which objectively discusses some of Abigail’s behavior toward Will that seems to be an obstacle for some of the fandom. I’ve linked this through a reblog because of cristiline's tags, which I address in this post. (Sorry this is such a clickfest.)
To what extent Will’s feelings for Abigail are genuine is a more complicated subject.
I’m torn between thinking their relationship was terribly underdeveloped for how important it is, and liking how awkward and fragile and human it is.
But it makes sense that they’d be so conflicted. It’s more tragic, in a way, that they were just finally starting to bond when Hannibal faked her death and framed Will for her murder.
Then in the fishing scene, he’s genuinely asking, I think, if she cared for him. It’s not because he’s confident in the answer. But he’d keep her secrets and try to catch her killer either way, so she can rest in peace.