The British Sky rider finished 12th in Oudenaarde, 49 seconds adrift of winner Peter Sagan (Tinkoff), but had harboured hopes of winning his first Monument.
Thomas was well-placed going into the race's last two ascents of the Oude-Kwaremont and the Paterberg, but he was unable to join the triumvirate of Sagan, Sky team-mate Michał Kwiatkowski and Sep Vanmarcke (LottoNL-Jumbo) when they launched at attack with just over 30km remaining. Sagan then soloed away to win from Fabian Cancellara (Trek-Segafredo).
Thomas's failure to follow the trio ultimately put paid to his chances of victory. "I should have been in that move that Kawasaki (Kwiatkowski) was in," the 29-year-old told Cycling Weekly.
"When he went, it was a case of sitting behind and waiting, I should have probably been there and am pretty confident I could have stayed with Sep, maybe not Sagan, but definitely Sep and then suddenly you're riding for the podium. It's such fine margins."
Thomas's eighth position in the 2014 edition of Flanders and his win at E3 Harelbeke last year pointed to his cobbled Classics credentials, but his refocusing on goals to concentrate almost solely on stage races meant that his cobbled form was somewhat of an unknown quantity prior to the race.
Indeed, the Paris-Nice winner hadn't ridden a cobbled race this season, but he still believed he could have won.
"I had four days ill off the bike last week but I knew I was riding well and was strong after winning Paris-Nice. I knew I'd be there or thereabouts.
"I felt strong, I can be happy with how the legs were, but I just didn't quite have that real top end, that punch," he added.
"I was following Fabian (Cancellara) on the Kwaremont but I lost his wheel just after that and that was it, he was away.
Watch: Tinkoff sports director explains how Peter Sagan won the Tour of Flanders
"Once you are in that chase group and there's one or two guys up the road, it's so hard and nobody wants to pull properly. You're racing for fourth.
"I think I can be happy given that it's just my first race on the cobbles this year. One week racing 15km climbs with (Alberto) Contador and then trying to do it on a k-and-a-half climb with Fabian is a bit different."
Despite his attention being on riding for GC, the Welshman confirmed that winning Flanders will remain a goal. "I just love this race. This is still high on my list of races I want to do well in."
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