Stupak has not kept his reasons secret. They just haven't been widely reported.

My mistake was corrected by MOJ reader David Nickol. Here is the language he sent along with a link to the whole interview:

Stupak said that House Speaker Nancy Pelosi had enough votes to pass the health bill without him and the bloc of six or seven votes he brought with him, and that she released some vulnerable Democrats from voting for the bill after he agreed to support it. . . .

Stupak told The Daily Caller that the president’s order does nothing to change the law as it’s written.
“You can’t. It’s the next best thing,” he said.

It was that or nothing, he insisted, saying he knew for a fact that Pelosi released certain House Democrats from voting for the bill after he and his bloc of six or seven votes swung into the yes column.

“A number of them came up and thanked me … said, ‘Thanks for getting us off the hook,’” Stupak said. “I’ve been around here long enough to know that the speaker, Democrats or Republican, always carries a few votes in their pocket.”

“So I had a choice: to come up empty-handed and a bill passes with language that I totally disagree with, or I do the next best thing.” http://dailycaller.com/2010/03/23/stupak-says-catholic-bishops-pro-life-groups-tried-to-use-abortion-to-defeat-health-bill/

According to the article, Pelosi claims that she never lets any Democrats off the hook, but this seems implausible to me. So I think Stupak is telling the truth.