Truthfully, I think it depends on the comic and what your trying to say. Right now it's just the tradition and it's hard to break the trend. It'd be nice to see a comic that tries to portray more average joes as heroes. Kinda like what they did for the X- 
Men's costumes in Marvel Ultimate X-Men comics. 
 
Another thing I should point out is alot of heroes are supposedly very active. It's not like their couch potatoes or work in an office. So with the right diet they really wouldn't have to work out. Their life style by it's very nature is a work out.   
 
One thing the article neglects to mention is the heights of alot of heroes. The average hero is at least 6 feet 1 inch. Would you believe that's how tall Professor Xavier is. 5' 11" is short in the superhero world. We do have few exceptions though like Wolverine whose a whopping 5' 3". 

I think it's interesting to see less muscular folks with super strength. It makes it more impressive that skinny little guy throwing a car.
 
But drawing the pumped up people is more fun.
And easier for bad artists to learn

Yes. Too many frail looking heroes nowadays.

" But John Stamos told me that physical appearance doesn't matter...  I think comics should show more heroes working out...and being sore the next day.  We see it sometimes, but it always feels like a disproportionate amount of time.  Let's see Colossus icing his shoulder after Fastball Special practice or Batman talking business but doing sit ups instead of sitting in an office chair.  At least kids would think, "I want to be just like those...oh wait, that looks like it would take a lot of effort.  Nevermind, I'd just rather be like Hank Pym...smart" "

They don't really need to be super muscular.. Look at Ambush Bug! The guy's more like a regular joe visually XD
 
Anyway, they shouldn't all have Superman-type of bodies...
Can't some be smaller, less muscular?
I don't expect, say, Animal Man or most of the super powered X-men to look like Hawkman "the barbarian"!

Makes me laugh whenever a new Green Lantern is recruited, not only has he/she the ability to overcome great fear, he/she is built like a brick sh*thouse. 

You know whose physique and physical appearance in general has always fascinated me?  Amanda Waller.
 
The traditional superhero, from the golden or silver age, is generally white, male, thin, tall, and well built.  Amanda Waller is the virtual opposite: black, female, overweight, short, and generally lacking in muscle definition.  That is not to say that she doesn't have any muscle under all that superfluous flesh, she certainly does.
 
And yet she commands no less respect than many of the more powerful characters she encounters.
 

" @XFan616: hey, anything to get fat, non-exercising, fast food addicted, lazy kids up off the couch and out the door I mean, they shouldn't be made to feel bad......but they aren't going to get any healthier reading books that tell them to "Love themselves no matter what!"  if that self if morbidly obese and eats pizza for breakfast    on a side note, I'm really sick of this whole "people have the right to be fat" mentality that's surfaced in the past few years I think everyone should love who they are and how they looksbut it's horribly unhealthy to eat crap and not exercise even if you're thin "

Honestly that't always been kind of annoying...w/ superman being the main offender. While Reeves truly captured the hero 4 me...Routh didn't. I mean Superman is built, he wears over-sized suits to make Clark look so small, Routh looks like i could prob mug him on the street. With IM or Spidey the actors made since, 1 starts off a geek who's transformed, the other is basically a rich guy (who would do wuts needed ta look good 4 the ladies ect ect) inside of a suit, any fat dude could wear a suit if u wanna b technical. I wanna see more like Blade's Wesley Snipes, or Tom Welling. People who look like they fit the bill. 

I think they should all be fit but not necessarily completely blown up with muscles..