The Wales international was sent off after kicking out at a ruck during Saturday's 36-25 win over Harlequins.
"It was a soft red card because players have been told that you can't flash feet into rucks now," said Baxter.
"Even if you genuinely think you can go for the ball, if you connect with someone's head you're liable for a sending off," Baxter told BBC Devon.
The 24-year-old was given an eight-week ban in March after making contact with the eye or eye area of Dan Cole during Wales' Six Nations loss to England.
"Tom's been a bit unfortunate," added Baxter of Francis, who had come on as a replacement.
"There's no malice there, but the reality is that players have been told about it and it's a habit that they must get out of."
Exeter head coach Rob Baxter has backed prop Tomas Francis after his second red card in six months.