Because they felt "it was time", and the studio decided to head in a different direction.
From their press release
As we enter into an exciting new era focused on the next Star Wars trilogy, Lucasfilm has decided to pursue a new direction in animated programming. We are exploring a whole new Star Wars series set in a time period previously untouched in Star Wars films or television programming. You can expect more details in the months to come.
After five highly successful and critically acclaimed seasons of Star Wars: The Clone Wars, we feel the time has come to wind down the series. While the studio is no longer producing new episodes for Cartoon Network, we’re continuing production on new Clone Wars story arcs that promise to be some of the most thrilling adventures ever seen. Stay tuned for more information on where fans can soon find this bonus content. In the video below, Supervising Director Dave Filoni offers a peek of what is to come in Star Wars: The Clone Wars.
Disney saw fit to go in a "new direction" in the animated programming, arguably looking to focus on a slightly younger demographic (gotta hook those kids).
It sounds like the mature themes of The Clone Wars may have been a bit much for what Disney would be willing to air on their own networks, but did not want to continue creating content to be aired on a competing network (Cartoon Network is owned by Time Warner).
This is backed up by a quote from Netflix's VP of content acquisition:
“The series really aged up over the years,” said Sean Carey, Netflix vice president of content acquisition. “It went to a darker place and didn’t fit the Cartoon Network brand any longer. So it was a hidden gem that Disney brought to our attention, and we jumped all over it.”
LucasFilm's Animation studio is not huge. They can't work on too many things all at once, especially since many of the production staff (from producers, writers, on down) had now been tasked with Star Wars: Rebels.
The show had run five full seasons and had begun production on the sixth. The Clone Wars, themselves, only lasted three years in-universe. There were, of course, more stories that could be told, but as time went on, they would likely start bumping into an issue of time frame eventually.
According to Lucas (take that as you will, given his history of changing his mind on everything), there were originally only 100 episodes planned.
TV Guide: And you're going to do a hundred episodes?
Lucas: We're going to do a hundred episodes. I think we're on [No.] 40 right now. We'll probably end up with 50 to 60 episodes before we start to put it on the air. We'd like to put it on next fall, in about a year from now, but we'll see what happens.
This was backed up by another quote from an interview a few months later:
CS: Do you see the show going on for a long time? It obviously takes a long time to produce computer animation.
Lucas: We’ve been doing this for three years. We have one year finished, we’re in the middle of the second year. I’ve written the third year. We expect this to go on for at least five or six years.
So, it sounds like they were likely either already past, or pretty close to their initial plans for Clone Wars stories anyways.