Ireland international Walters twice headed into his own net - just before halftime and then on 62 minutes - as Chelsea cruised to a 4-0 Premier League win at the Britannia Stadium.
The 29-year-old, who has netted seven times at the right end in all comeptitions this season, capped his miserable afternoon by wasting a late spot-kick.
"We all have bad days," Pulis told the BBC.
"He had a bad day in terms of things not going his way but he was still brave enough to pick the ball up and take the penalty, which is what he is all about."
Walters gifted Chelsea the lead when he beat goalkeeper Asmir Begovic in trying to clear Cesar Azpilicueta's chipped cross.
Begovic, who has been in outstanding form for Stoke this season, was left dumbfounded again in the second half when Walters headed in Juan Mata's corner under pressure from Frank Lampard.
"This football club looks after its players," Pulis said.
"He doesn't have to worry at all, irrespective of what people say outside the place - the place is a good football club. We treat it as a family and Jon will be fine."
Stoke's first home defeat in the league since February left them in 10th place.
- Sports & Recreation
- Asmir Begovic