Boonen initially finished fifth in Sunday's 259 km Paris-Roubaix but was promoted to second behind Switzerland's Fabian Cancellara after three riders were disqualified for passing through a lowered train barrier.
Despite his promotion, the Quick Step rider was unhappy with the disqualifications.
"It was the job of the stewards to stop them. I also would have crossed the barrier," he said.
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Boonen, who has revived passion for the sport in his native country, had no regrets after failing in his bid to achieve a unique double victory in successive years.
"Some people seem to think Tom Boonen has no right to be tired. But there is no shame in being tired. I'm not superman," he said.
Boonen is now setting his sights on the Tour de France in July, where he hopes to vie for the green jersey awarded to the points competition winner.
"I had to retire from the Tour last year and it's still stuck in my throat," the 25-year-old added.
"I now dream of winning stages and the green jersey.
"When I was in the velodrome at the end of the Paris-Roubaix, I was already thinking of the Tour de France."
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