The two sentences have slightly different meanings to do with the circumstances in which they might be asked.
Are you usually cooking at weekends? makes sense as a question to someone who might be expected to spend the whole of every weekend cooking, such as a part-time chef or someone who loves to cook but has to do other work during the week. Consider 'I am usually working on Tuesdays'. That implies that work is the major activity on Tuesdays.
Do you usually cook at weekends? does not suggest that cooking is the predominant weekend activity. A husband, whose wife cooks meals during the week, might wish to cook for her at weekends. The question 'Do you usually work on Tuesdays?' could be downright insulting - especially if asked by one's boss.