tl;dr: My suggestion is to establish dialog, go to couples counseling to help learn the skills that may be lacking in one or both of you and to identify if there are any ingrain social conditioning that the both of you thought you had risen above.
Most comments here are from males who make more than the female. The thing not being said is the societal expectations we are conditioned with, and the switch in "roles" here. Her being the "breadwinner" and even though you also make good money. You say:
>> at first, I was jealous and a little bitter, and she was worried that I was taking advantage of the situation ... As for out salary, we decided that we would both spend as if we both made my salary, and anything above that, she would put in a rainy day fund
You did not mention the household chore division or any possible kids. So I will assume it is an average 2 income household; one where the female does slightly to moderately more household chores (I believe this is even more true for females in high power careers)
This would not seem fair to me, and I dont know if that is what is happening, but I would also suspect you taking advantage of the situation - not monetarily, because its not about the money, it's about her living both the "breadwinner" and "homemaker". While you also bring in money, the part I really cringed at was -> having set the spend limit to the max amount YOU make. She does all the contributing to the rainy day fund. I would have a problem with this even if you made more and her less because both are not contributing. I would have issues with it even if household chores were even. Many of the reply's here (by the I assume male, with a wife) dont see it as a problem in their situation. However, they are fulfilling their "role" and society would mostly think it petty of them to expect her to contribute - which I personally think is unfair. I would also insist I contribute in order to feel parity.
You are on to something with the being bitter and jealous at first, because we are conditioned to have households where the male makes more, so it's easier for the male to be in his "perceived rightful role as breadwinner" and have zero problems sharing the money because that's his "role", the wife is doing the house/childcare and maybe part-time work for fun money. Everything is as we are told it should be.
You may be doing little micro-aggressions and not know it. She may sense this and think you are taking advantage of the situation but can't quite put her finger on it - I'm going to go out on a limb and say it really has absolutely nothing to do with money from her side. That's the only thing she can point too because the other may not be obvious to either of you.
I'll try to explain, from my personal experience as a highly paid female.
Im not sure how much males understand their insecurity with females making more than them. I thought this was for my fathers generation. Then I tried dating. I dont mix work with personal life and dont want to go home and talk tech. So most guys will make less, I dont care - at all as long as he has a job and can take care of himself.
Things are great until they find out how much I make and then would pretty much disappear. Sometimes slowly; sometimes before I finish the sentence. I figured they were just insecure and did me a favor. I would find someone else. Then I really did, a friend who made 1/4th what I did working in the public sector, my main attraction was that I thought he was completely, fully, secure in his masculinity - others couldn't threaten him with challenges to it - it was hot. We got closer and I disclosed details of my work and pay (which I avoid with most people), the instant look of dejection in his body language and change in his voice said all I needed to know. He started seeing someone around his same pay grade a few months later. I think a lot of guys want to believe it won't bother them and truly believe it since most never have to test it. I have the very unfortunate experience of making it real for them.
I dont know what experiences you wife has gone through or what expectations she (subconsciously?) harbors, but I have had to learn conversational gymnastics around what I make, especially around males that I know make less and who I actually want to be friends or spend time with - Im not sure they realize the change in the way they see me when they find out - but it's not fun to feel constantly rejected or unintentionally intimidating just for living my full potential; I wont downgrade myself or be the one to compromise to make males feel better about themselves either, it's not my job. My responsibility is to myself, to provide for my survival needs. And I wont settle for the few guys that are more than willing to sit on the couch playing video games all day while I pay the bills, clean and provide dinner. Im just not sure many males are fully aware these issues exist.