You can, actually use the form you're talking about but you can't use "are". The problem is that a person isn't described as being a job, they have a job. When you use "are" in "What job are you?" you're saying that that job is part of what they are, which isn't really the case.
When we say "What is your job?", we are asking "What is the job that you have?", so we're not saying that they are that job.
So, you can say:
What job do you have?
It's a bit unusual a form but there's nothing wrong with it.
Here's an example that might happen... Say you're in a job interview and the interviewer is reviewing your resume (CV):
Interviewer: I see you worked at company X, what job did you have while you were there?
To make it slightly more confusing, when you talk about someone's line of work or trade, we do often use "to be".
I am a musician.
You are an engineer.
She is a doctor.
We/you/they are lawyers.
The odd thing is that it's difficult to invert these answers into a question that's not ambiguous. "What are you?" is the simple question, as Victor pointed out in his answer, but nothing about this question requires that the answer be about your line of work. People "are" a lot of things - they are their gender, their ethnicity, their nationality, etc.
In context, it's possible to say:
I'm a doctor, what are you?
But if you were talking to someone and just said "What are you?" without the context of discussing careers, you would likely be asked to explain your question.
The most common phrasing I've run into if you're trying to ask someone what their career is, rather than their job, is
What is your line of work?
What do you do?
Even without context, though, the second option can be a bit confusing though it's certainly less confusing than "What are you?" If you know where someone works, you could certainly say:
What do you do at Company Y?
And, yes, you can certainly say "What is the flower's color?"