I think you've handled this quite well. The comment may simply indicate that he was unsatisfied with the overall results, and you were simply there to take the heat. It does not need to mean that the CEO is unsatisfied with your performance - he would've made that more clear if it was really an issue.
Some CEO's shoot from the hip. In these individuals I observe an ability to cut the crap, quickly form an opinion, pick out problem drivers and pressure the right individuals. They judge situations and make decisions quickly - occasionally too quickly.
I find this type of CEO to be a bit... abrasive - and sometimes intimidating. But I also think that it makes them effective, at least in the small organisations I've been a part of. After all: The first thing you did in response to his comment, was open up about impediments.
In your position, I would feel hesitant to ask feedback on the specific conversation with the CEO, or to ask my manager what the CEO thinks of me. The manager wasn't part of that conversation and I'd be disinclined to give him a full play-by-play. (If you identified your manager as a blocking factor, he may have gotten an earful.) And I'd hate to come across as needlessly insecure (which you aren't). So I'd prefer to frame it as an investment in the success of future projects.
If you have the opportunity to talk to the CEO directly and informally, do so. I'd open with something like:
"I got the impression that you were not satisfied with the results. Is there something I could have done differently?"
But it isn't his job to manage your performance on that level. He may not be the right person to give you feedback. That is why I would definitely talk to my line manager about this. We regularly evaluate projects where either of us felt there was room for improvement. I would schedule a one-on-one and basically ask him the same question. Is he satisfied? What can you do differently? It helps to bring a specific issue that you would like his advice or backup (in future projects) on, such as your difficulty getting the co-founders on board. Prepare by listing how that was an issue and what you tried to remedy it.