At the end of the '09-'10 television season, Scrubs having a perfect comedy pilot and a pretty remarkable run, it still got canceled, not once, but twice.
After its seventh season, Scrubs was canceled by NBC, but it was picked back up by ABC due to its production deal. Scrubs' seventh season had been disrupted by the 2007-08 Writers Guild of America strike, like many shows that year. Since it got picked up by ABC after NBC dropped it, this meant it always had a second chance at cancellation. Its second cancellation was remarkably low-key, too; Zach Braff, the show's star, announced it on his Facebook page. However, by the time Scrubs had reached its ninth season, a large percentage of its original cast had left or been reduced to guest star roles. While guests (like Michael J. Fox, Scrubs' greatest guest star) had always been an important part of Scrubs, it signaled a shift in Scrubs that would impact its cancellation.
Scrubs' cancellation wasn't about ratings. No, the answer to Scrubs being canceled a second time lies in the creative decisions made for its final two seasons. Creator Bill Lawrence had tried to bring the show to an end several times, and by the time the ninth season was being planned, the original cast were trying to start careers unattached from Scrubs, which is why so many of them left or heavily reduced their screen time. The show shifted entirely from the hospital to the medical school classroom, creating an entirely different dynamic and feel to a show that had already tried to end multiple times.
A brand new cast was brought in for season 9, with star Braff absent for most of the season. Some favorite Scrubs. Most of the main cast of season 9, like Eliza Coupe, Kerry Bishé, Michael Mosley, and Dave Franco portrayed characters that had either only appeared in season 8 or were brand new to the show. This caused confusion and dissent among viewers, who saw the show as radically changed from its original premise. Lawrence saw the show as a different one from the original, too.
Scrubs was canceled in part due to ratings, but also due to the fact that it had radically changed. Lawrence wanted to move on, and its original stars and quirky characters had almost all left. When all is said and done, nine seasons for a show like Scrubs, which never dominated the ratings, was actually lucky for the little medical comedy that could.