Let's be honest, this is the entire reason.
I ask again, what's a comparable player who made the HHoF without having his career be cut short by injury or similar reason, who for all intents and purposes provided NHL quality play for 5 seasons?
Thomas became the starter for the Bruins in 06-07. His numbers weren't good. This was also the only season in his career he played 60+ games (which is important, especially when comparing him to other goalies in the HHoF).
The next season he provided adequate goaltending, per advanced stats and compared to backup Auld.
He then had his breakout season in 08-09, where he won his first Vezina.
The next season he lost the starter job to Tuukka Rask and allowed 5 goals in his only OG start.
The next season is his strongest case for the HHoF, when he won the Vezina and Conn Smythe.
The following season he was fine, but not as good as the .920 number seems these days. Boston was an incredibly strong team defensively, and the advanced stats again show him to be roughly replacement level. An okay starter, nothing more. His numbers were quite a bit worse than Rask's that season.
That's Thomas's NHL career. He retired, unretired, was among the worst starters in the league for a season, and retired again.
Unless you want to count the lockout year he played for Jokerit, nothing he did outside of the NHL makes a case for an HHoF nod. He was an utterly mediocre player for the U.S. national team as well.
His HHoF case consists of two seasons. In between those two seasons, he was demoted to backup.