I'm not saying he didn't take anything, or that Ortiz is clean beyond any doubt, but that doesn't mean the allegations aren't suspect at best. What did Ortiz allegedly take? Even Rob Manfred stated that the 2003 test results had "legitimate scientific questions" and that some positives could have been triggered by legal, over-the-counter supplements.
Ortiz was radically inconsistent before 2003. He was a dead pull power hitter with a massive hole in his swing known to virtually every pitcher in the American League. If he were so consistent, the Twins would not have released him after 2002. He probably would have signed on somewhere by Spring Training, but he had virtually no prospects until he met up with Pedro in the Dominican Republic. Even in '03, he was a spot player, before settling in as the Dan Hurley in the second half of the season. He even requested a trade because he wasn't happy with how he was being used. He was a "nobody" back then, which was not the case in 2009 when the report was made public and the NYT could make a headline with his name.
His consistency came when he fixed the hole, focused on hitting to all fields, and accepted the fact that his days at 1st would be fewer and farther between going forward.
Finally, Ortiz is in the Hall of Fame, which shows how much credence the baseball writers gave the 2003 report.