I could see it escalate into an arms race: if the new norm for watching videos will be to automatically skip sponsored segments by some popular software, the sponsorship offers will either dry up, or the resulting sponsorships will be designed to be more difficult to skip (eg. by making content creators incorporate them throughout the video in many small chunks, or as overlaid audio/video, ...).
Similar to what happened to web ads in communities that tend to run adblockers: more and more obnoxious advertising (intersitial ads, animated ads, etc.), advertising incorporated into content (ads-as-content like on Reddit), cross-site tracking and retargeting.
I tend to manually skip sponsored segments (especially for snake oil like VPN services!), but I'm not sure if writing automated software for this is the right thing to do in the long term.