They can be used interchangeably without much noticeable difference in my opinion!
"You can use the present simple or continuous to say how somebody looks or feels now"
^^^^From an online search
However, if I had to stop and give particular attention to the phrases in the way I use them....
When I see someone I hardly know I will always say "How are you feeling today"
When I see someone I know I will say either choice "How are you feeling today" or "How do you feel today"
I can't explain why but when I use [How do you feel today] it's a phrase I say among people with familiarity.