A website done in Flash is not really a website. Would you consider a PDF document sent by a web server to be a website?
A website done entirely in flash will still have the <html> tags in the source, so therefore it is really a website. Also many websites utilise flash in parts, some pieces of interactivity which would be very difficult to do and have big overheads in HTML/CSS/javascript can be done very easily and efficiently in flash. Not to mention the fact there are less cross browser issues.