CNET's download site is known to distribute adware, so I strongly recommend against its use. That said, it doesn't look like the f.lux download from that site currently uses the CNET adware installer. If you haven't noticed any ads being injected into pages where they shouldn't exist, or obnoxious pop-ups that weren't there before, you're probably okay. If you want to make absolutely sure, you can run a scan with AdwareMedic, as dwb recommends, or try the manual instructions for finding and removing adware in my Adware Removal Guide.
(Fair disclosure: I may receive compensation from links to my sites, TheSafeMac.com and AdwareMedic.com, in the form of buttons allowing for donations. Donations are not required to use my site or software.)