It is generally neutral but could be positive or negative, depending on context and who makes the judgement. Any time you describe someone with a single adjective you run the danger of sounding accusatory. For example, if you say someone is "talkative" it might sound a bit insulting even though there is nothing wrong with being talkative. To make an adjective sound better, soften it up a bit:
She does know how to flirt.
She has perfected the art of flirtation.
She can be flirtatious now and then.
I enjoy watching her flirt. She is a natural.