Help, my newly adopted Lilou has URI and it just won'5 go away!

I adopted Lilou grom a shelter about 5 weeks ago now. They had warned me that one of the cats in the toom she stayed in had a "cold", and to come back for medicine if she developed symptoms within 2 weeks. Unfortunately, I missed the signs and when she started having some sort of congestion, I thought she was just snoring. 2 weeks later, she started sneezing a couple of times and thenall of a sudden her eye got really bad. I took her to the vet immediately and she prescribed antibiotics and some sort of eye ointment.
The problem is my poor Lilou has had a hard time adjusting (being sick probably didn't help) and she doesn't completely feel comfortable around me yet. She is very skiddish and doesn't like being carried.
She immediately hid under the bed once she came back from the vet, andI eventually had to force her out from under there to give her meds.
I had to put her in the bathroom and leave her there for now as it's the only place I can get to her (let'/ just say that getting her there left me with some serious scratches!)
She'/ getting better with me giving her meds but I am worried that this will leave her afraid of me. I try to pet her a lot before and after giving her the eye meds, and often go in the toom just to be with her (so that she doesn't see me as the evil person who always comes into manhandle her), but I can see that she fears me as she always jumps in the tub when she sees me come in. She seems to forgive me each time thoughand I make sure to never leavebefore she starts purring again when I brush or pet her. Do you think there's a chance this experience will prevent her from bonding with me? I would hate for her to live in an environment where shehasto be afraid of me.
My other worry is that she doesn''t eat much and it takes me an hour at least to get her to eat and she never finishes her portion. Should I stop and give her the meds with a syringe? Or is it ok if she doesn't get the whole dose each time?

Thank you for your advice. She's my first cat and This adoption has not been plain sailing so far (although I wouldn't change her for the world!)

As far as the meds go, I don't think you would necessarily have to give them with a syringe, but she probably does need the whole dose.  So mix the meds into a tiny bit of food and then give her the rest of the food after she eats the medicated portion.

I think she'll probably still bond with you.  She just doesn't feel good and that's going to mess with her mood.  After she gets over being sick, she'll probably bond with you just fine.  I mean, let's be honest.  I would be less likely to get friendly with someone I met while I was sick until I started feeling better.  So to me, this seems like a perfectly normal reaction.

Thank you for your response Alicia88. I already do the small portion mixed with the meds. I have tried everything I could think of: tuna, salmon with lots of juice (she seems to lick her food more than biting into it) mixed with little bits of actual fish and dry food as it seems to be the smell recognized the most. Unfortunately, I don't think I can just mix the liquid with dry food only though. So besides using a syringe, I'' not sure what else to do. I really hate the idea of forcing her to take it though.

Have you tried putting it in treats? A couple of times, I've gotten my boys these treats from Wal*Mart. They come in tiny little packets And they're like mush. Fancy Feast lickable something or other is one of the brands. I can't treatment exactly.
The reason I'm suggesting this is how well Connor and Murphy eat them. Every kind of soft food I have given them - they leave some. They never finish it. But those treat things? They lick the bowl clean. Literally. The bowl looks like it had never had anything in it.

Thank you! I will definitely try that! On a positive note, Lilou's eye seems to get better (although the littlest amount of stress like me coming to her with the eye drop or simply walking in the room and her eye starts watering again. She's a sensitive one! I've also bought a vick's humidifier. I hope this'll help for her nasal congestion.