I think Rory had doubts, yes. He spent most of "The Vampires of Venice" disliking the Doctor quite a bit. He only started to warm up to the Doctor when the Doctor ordered Amy back to the TARDIS, and I think there were two reasons for that: first, of course, that he was trying to keep Amy safe, but secondly because their interaction in that scene was very much not as potential love interests. If anything, the Doctor sounded more like a snappish father playing the "Because I say so," card, and Rory would know first-hand that Amy does not take that sort of thing from a boyfriend.
Rory's doubts were also a major factor in "Amy's Choice," where he still wasn't entirely sure how Amy felt towards him. You can see a lot of uncertainty and self-doubt in the way he informs the Dreamlord that the Doctor is the odd man out, not him; there's a tense pause when Amy says, "I've chosen, of course I've chosen," and then has to tell him, "It's you, stupid!" If you watch him at the end of the episode, right after Amy tells him that she gambled her own life to get back to a world where he was still alive-he honestly didn't know that she felt like that. (Which is, of course, largely on Amy, who has Issues. This is, after all, the woman who turned "stupid" into an endearment because she had trouble saying it directly, and who suppressed her feelings about her daughter until they finally exploded and led her to flat-out kill Madame Kovarian-who had it coming, but still. It's really a good thing she didn't get together with the Doctor; the Lack Of Communication Singularity could have consumed the universe.)
I think the one thing that Rory never doubted-the thing that he may be constitutionally incapable of doubting-is that he loved Amy. Which is why I think that Amy's hallucinations in "The Doctor's Wife" did come from her own brain. I mean, Amy is screwed up. And Amy knows she's screwed up; if nothing else, she's the Girl Who Needed Five (Moderately Toothmarked) Psychiatrists. In the cracked universe, in "Amy's Choice," she admitted that she'd never actually been able to tell Rory she loved him until she saw him crumble into dust right in front of her. (Since we see her say it quite easily in "The Big Bang," that was almost certainly related to the crack eating her family. I suspect her spooking at marriage is also related-marriage makes you a grown-up, grown-ups disappear-but I don't have as much support for that.) She also knows that Rory protected her for two thousand years and never even resented it.
The thing about being beloved, when you're a touch messed up, is that you wonder why. Why, why in all the worlds would a man like Rory-eternally faithful Rory-love you? What does he see that's worthy of that sort of devotion? What makes you worthy of him? And when you start wondering that, there's a little voice that says, "You know what? You aren't worthy. And sooner or later, he'll realize. Sooner or later, you'll do something-betray him, forget him, behave thoughtlessly towards him-and he'll wake up. He'll see you for what you really are. And he will DESPISE you."
So, House made that happen. I suspect that Rory's hallucinations-you know, the ones he must have had to be able to say, "It's just messing with our heads, stay calm"-probably had more to do with hurting or killing Amy, or other connected things like turning into an Auton again.
Rory's doubts were also a major factor in "Amy's Choice," where he still wasn't entirely sure how Amy felt towards him. You can see a lot of uncertainty and self-doubt in the way he informs the Dreamlord that the Doctor is the odd man out, not him; there's a tense pause when Amy says, "I've chosen, of course I've chosen," and then has to tell him, "It's you, stupid!" If you watch him at the end of the episode, right after Amy tells him that she gambled her own life to get back to a world where he was still alive-he honestly didn't know that she felt like that. (Which is, of course, largely on Amy, who has Issues. This is, after all, the woman who turned "stupid" into an endearment because she had trouble saying it directly, and who suppressed her feelings about her daughter until they finally exploded and led her to flat-out kill Madame Kovarian-who had it coming, but still. It's really a good thing she didn't get together with the Doctor; the Lack Of Communication Singularity could have consumed the universe.)
I think the one thing that Rory never doubted-the thing that he may be constitutionally incapable of doubting-is that he loved Amy. Which is why I think that Amy's hallucinations in "The Doctor's Wife" did come from her own brain. I mean, Amy is screwed up. And Amy knows she's screwed up; if nothing else, she's the Girl Who Needed Five (Moderately Toothmarked) Psychiatrists. In the cracked universe, in "Amy's Choice," she admitted that she'd never actually been able to tell Rory she loved him until she saw him crumble into dust right in front of her. (Since we see her say it quite easily in "The Big Bang," that was almost certainly related to the crack eating her family. I suspect her spooking at marriage is also related-marriage makes you a grown-up, grown-ups disappear-but I don't have as much support for that.) She also knows that Rory protected her for two thousand years and never even resented it.
The thing about being beloved, when you're a touch messed up, is that you wonder why. Why, why in all the worlds would a man like Rory-eternally faithful Rory-love you? What does he see that's worthy of that sort of devotion? What makes you worthy of him? And when you start wondering that, there's a little voice that says, "You know what? You aren't worthy. And sooner or later, he'll realize. Sooner or later, you'll do something-betray him, forget him, behave thoughtlessly towards him-and he'll wake up. He'll see you for what you really are. And he will DESPISE you."
So, House made that happen. I suspect that Rory's hallucinations-you know, the ones he must have had to be able to say, "It's just messing with our heads, stay calm"-probably had more to do with hurting or killing Amy, or other connected things like turning into an Auton again.
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