It's not that Ilya doubts Shane's love for him. He's aware that Shane loves him. It's just that, in his darker moments, he doesn't think he should and, even in the not so bad moments, it's sometimes hard for him to understand why. When he's suddenly on the third (fourth?) day of not being able to rise from bed, unable to bring himself to shower, unable to even get up to pee, curtain drawn against the summer sun, with Shane bringing him soup and feeding him spoonfuls Ilya doesn't want but accepts for Shane's benefit, he does think it would be easier for Shane if he didn't love him. When he tries new medication and his fucking dick stops working, preventing him from giving Shane the only thing he knows he can do better than anyone else Shane could find (someone who didn't come with all this fucking baggage), it's hard to see any reason why Shane would want to stay when he can't even give him the one thing he's good for. When the world turns so grey that Shane's freckles start bleeding away into the rest of his skin, he feels like crying but he can't quite get there, the numb weight on his chest keeping him from even that much. And through it all, Shane holds him and strokes his hair, and whispers "I love you. I choose you. You're my favourite person. I would choose you a thousand times over." He even writes it down on a piece of paper, leaves it in Ilya's line of sight, when he has to go to practice, Ilya insisting he go, Shane hesitating, making him promise to call if anything changes, if he needs him here. Ilya says he will, knowing full well he won't have the energy to lift the phone, he doesn't even have the energy to lift the piece of paper, the one he knows says "I choose you" in Shane's chicken scratch handwriting. Just knowing it's there does help a little, though.
When he's feeling better, a few days later, he takes the note to a tattoo parlour, inking it over his heart as a permanent reminder that although Ilya doesn't always understand why, Shane does choose him. Would choose him a thousand times over.