Before the series started, I understand. She knew that there was danger out there, she should have told Clary but she didn't so that's irrelevant, and Clary didn't understand her mother's worry. Most parents are protective of their kids, and she knows she has a reason to be more careful. After Clary was brought into the Shadow World and began training, Jocelyn let up a bit. She felt she had, if not less to worry about, then a reason to trust Clary to be careful.
Her whole Simon problem, any parent would say that. He'll I would have said that in her shoes. Her daughter just went to her possible death and she had every right to be freaking out and Simon was the easiest and closest target. That's why I don't blame Jocelyn, she had a reason to be terrified.
I think what you say is true, but I actually understand why she behaves like that. All mothers have that protective instict with their children, but she already had to deal with the death her parents, the transformation of her best friend (then lover) into a werewolf and the loose of her first child (yeah, loose, because Jonathan could've been a normal child if it wasn't for Valentine). It is completely understandable why she wanted to keep her daighter safe.
Jocelyn just wants to keep her daughter safe, and considering her background, it makes a lot of sense that she would be even more protective and clingy than the average parent. She's already lost a child, and she knows the world's an even more dangerous place than most people think it is. Not to mention, isn't Clary ~15 in the books? I don't think it's outrageous of Jocelyn to be telling her to do a lot of the things she does, and I don't really think that's "controlling". I'd maybe call her suffocating (even then, though, she allows Clary to go out with her friends alone in NYC), but as far as things are, Clary's not even considered of-age Nephilim-wise, and trying to run around doing things even Isabelle, fully-trained, wouldn't be allowed to do.
I definitely think she made mistakes, but they came from a place of genuine love and concern for her daughter. All parents make mistakes--they are human, and thus imperfect. But everything she did, she did with Clary's best interests in mind.
It's times like this that I wish we could get more adult perspectives in the series. Obviously it's a YA book, so that's basically out of the question, but how youths perceive the choices of adults/parents, and how parents and adults are actually thinking, tend to be very different. I enjoy that you get brief views of that by, for example, comparing how Magnus views Jocelyn and her choices, as compared to Izzy and how she views/treats Jocelyn and her choices. Unforunatey, because the narrative is told almost entirely by younger people, I think it's very easy to only take the text at word value, and believe whatever is stated as the truth or the absolute opinion of the story as a whole, when in reality it is only what that one character thinks or believes. A lot of kids and teenagers don't tend to be sympathetic when it comes to their parents and other adults, and I think Cassie demonstrates that pretty well.