Filler (as in, stuff exclusive to the show) is only bad if they treat it as filler (pointless padding). Shows should use those episodes to develop the characters more, maybe the side ones that the original author never did, or tell an interesting story. Yu-Gi-Oh's Doma and Noa's storylines are some nice examples of that. If it counts, as does the second half of FMA since it went its own route compared to the comic (and now that part of the comic is being animated, so you can pick which one you like better) and other similar shows (like Trigun)
However, when it's like Naruto's and just pointless uninteresting stuff to waste time,then yes, it's bad. But ruined? I doubt it, since the shows still remain to be popular and people just skip over that stuff anyway usually and pretend it doesn't exist.