Agreed. The comment in the letsrun Zurich recap ("Flanagan has been tremendous on the roads and XC the last year, but has not run great on the track since her Olympic medal in 2008 and her coaching switch soon after.") is inaccurate.
Check out her performances post-Cook here at the bottom of her bio on the USATF website:http://www.usatf.org/Athletes/Bios/Flanagan_Shalane.asp
A US indoor record of 14:47 in 2009, 14:49 last year, 14:46 and 14:45 (coming within a half second of her 5K pr) this year, and running 30:39 for 10K this year, which is the #2 time in the world in 2011, #3 time in the US all-time (behind her own 30:34 and 30:22 from 2008), and faster than any other US woman has ever run.
I think it's fair to say she hasn't improved since leaving Cook and her 5K times seem to have plateaued, but she's clearly still one of the best female runners in the world on the track and off.