Don't forget that there are actually two Clone Wars series. The first one was the 2D animation, which I think is what people weren't so much sold on. From what I remember, it was only after they had made the 3D animated series that people started to really take notice of it. I'm not even sure if they share the same continuity.
To be fair the first "series" was pretty much just a collection of loosely connected 3 minute shorts. The second "season" was more or less one rather long episode with a fairly contained narrative that alternated between two plots. It wasn't really a show in it's own right so much as a tone poem for the world and a promotional lead-in for what was the new film at the time.
The 3D series was a much more traditional show of 30 minute episodes. Even then I think it wasn't until the second or third season that it's popularity among the fanbase really started to pick up the pace. Much of the resistance to the show early on was for all the usual reasons fans resist prequels:
"there's no tension or drama when we already know when they die" "it doesn't add anything to the narrative" "it explains too much!" etc. etc. None of those claims bore out in the long run as the quality consistently improved.
So yes, while being a prequel of something doesn't automatically mean a fandom is going to unequivocally hate it, it's certainly an uphill struggle. We're seeing a similar shift now with Rebels, though this time with the uptick coming much earlier in the run, thanks mostly to the return of Ahsoka at the end of season one, but also a lot of good will earned by the same creative team as TCW.
Indeed, Ahsoka is practically a paragon of this uphill battle as she was almost universally reviled when she was introduced at the beginning of Clone Wars, but fast forward to the end and all of a sudden she's THE breakout character and by far the most popular among fans of all stripes.
That's the difference between movies and TV shows though. Movies have to win you over in just a few hours, while a TV show can have dozens, even hundreds of hours to do so. Clone Wars was a show that took advantage of that extra time to blaze new trails and build a following, while the likes of 'Enterprise' mostly (but not entierly) squandered those same opportunities.