Most thing... or better said many times, things in comic book are illogical... powers, their use and their origins... you can try to get away with it, try-a make a logical explanation about it, but still they're implausible.. most of the time.
What was so great about the first season of Heroes was exactly that, a drama/action show based on the illogic of comic books (or how you put it Comic book logic) that managed to create and compel an attractive appeal to both comic book geeks and "cool" hip people... while still being a geek fest.
You have people running around with powers, trying to save or destroy the world...traveling to a horrible future... that many people tuned in, watched and were in no risk of being called a "geek" because it was good TV... that indeed use comic book logic: the powers themselves (which it's the primary and most important thing about the show) are comic book logical... the saving the world and the bomb (many themes that some can say were inspired or rip off from "Watchmen") are so comic book-y in their essence... but it was still cool to watch.
... you can draw so many parallels to "X-Men" within the show, and still have them play out, that many people enjoyed... not just comic-book geeks.
Yes, there are things about comic books that are really annoying (dead people that weren't dead... or were resurrected in the most stupid way) that weren't used in the first season... but believe me:
Heroes is in essence a superheroes comic book
"When Gotham is ashes, you have my permission to die." -BANE