Your cat does NOT hate you!!!!!!!!!!!
First of all, welcome to TCS, and I'm glad you found us! And thank you for rescuing a shelter kitty!
As a "dog" person, you're used to an animal that immediately loves you, that seems to show her appreciation in very immediate and apparent ways, and that is motivated to make you happy. Cats are quite different. You have to earn their love and trust, because they are independent and proud. They do show they love you, and they do share their appreciation - but it's something that happens over time, not right away.
They are social animals, but they are not pack animals. Unlike with dogs, they do not come preprogrammed to look to the alpha for leadership, and they do not come preprogrammed to make you happy. But once you've earned that trust - it's a very different kind of bond than you get with a dog. And when you've worked so hard to earn it, it's really rather remarkable and incredible and something that feels quite wonderful. In fact, I'd have to say that it's a bond between human and animal like no other.
Cats are not genetically programmed to make people happy. (Can I say this like a million more times?
) They are genetically programmed to keep watch over their territory. So changing a cat's territory is traumatic to kitty. Their initial reaction is fear. Your kitty has just been very traumatized, being moved around. He was happy and loving because he'd made the cage his territory, and he knew it was safe.
For now, his territory is his crate, and the bathroom. He started to explore a bigger territory - and in his mind horrible things happened to him! He got trapped, a strange person pushed and shoved and him - and that strange person's smell is all OVER the place!
As he comes to feel safe, he will slowly expand his territory. But the crate or the bathroom may be kitty's territory for a little while. Cats operate on their own schedule, so the less you have some kind of time frame in your mind, the happier you (and he) will be.
But until he's learned that the human in the same space with him is not any kind of threat, he'll probably keep to a very small territory. Or, if you leave the bathroom door open at night and when you're not away, he'll come out to explore when you're not around.
What you can do to help him learn that you're not a threat to him and to make him more comfortable:
1) Sit on the bathroom floor and read out loud.
2) Get a radio and tune it to a classical station, playing softly in there.
3) Ignore him at first when he shows interest in you.
I KNOW you want to pick him up and let him know how loved he is - but he doesn't get that yet! First he needs to figure out you don't actually mean him harm. As he figures out you're not a threat, you can work on getting him to associate you with good things:
4) Get a couple of old t-shirts really sweaty. Put one of these under his food dish.
Use the other one to leave treats out on for him - you don't have to be there when he eats them. Put the t-shirt down, put treats on it, and leave. Or sit there on the floor reading. If he doesn't come out, leave them for him to eat after you've left.
Cats learn by association. It's totally different than with dogs. So by getting him to to associate you with food and good things, that will help him come around.
5) If he comes out of the crate or bathroom and is wherever you are, don't look him in the eyes. This is a sign of aggression. Look at his forehead or over his head. Better yet - if you're on the floor reading out loud or something, ignore him, and stretch your arm out a little bit - PALM DOWN. For dogs it's palm up - for cats, palm down is less threatening.
6) If he sniffs, let him - don't try to pet him. The first thing you need to establish is that you don't want anything from him, you don't want to do anything to him. Once he gets this, then he'll let you know when he wants attention and/or pets by "bumping" you. He'll either rub up against you - or he'll literally bump your hand or arm or leg with his head.
7) When you get to the point where you're petting kitty, do NOT pet kitty's tummy. Some cats do like to have their tummies rubbed. Some cats come to enjoy it. But at first - avoid it. Cats get overstimulated very easily. They often "drop" to their sides and roll - and it looks like an invitation to rub a tummy. Especially to dog people. This is rarely what they want. Our kitties flop over, and still want to be petted on their cheeks - sometimes under the chin. Cats have scent glands in their cheeks - it starts at the back of the gum - and this scent gland puts out "friendly" markers. For some reason they love having this stimulated. But when you see the end of their tail begin to flick, stop. Otherwise kitty may give you a quick bite. Some cats are good about this - giving signals that they've had enough, or that they're starting to get overstimulated - other cats aren't. And the way they then communicate they've had enough is to a) give you a quick bite (often it's more like put their teeth on you - but if you're new to kitties and he's really overstimulated, he may give you an actual bite - but not break skin - enough to let you know "stop." ) or b) put their paw on your hand. Again - it's the opposite of dogs. With cats, the paw on your hand almost always means "stop," not "more."
The Feliway should really help your kitty adjust to his new environment without as much stress!
Most importantly - feel free to ask lots of questions! I didn't know a thing about cats - and they are SO different than dogs, and if you work on changing your expectations and just let kitty be kitty, and go through his adjustment process, you'll be converted to a kitty lover in no time at all - and you'll be amazed at the bond you'll have with your new baby boy.