Penalties either side of the break from Marko Arnautovic and Peter Whittingham ensured the spoils were shared in Wales on Saturday, with the first spot-kick given for a clumsy tackle from Kim Bo-kyung on Peter Odemwingie.
Cardiff's penalty also appeared soft and Hughes was disappointed by the decision that went against his team, suggesting that Fraizer Campbell "looked" for contact from Steven N'Zonzi before going down in the area.
"The neutrals in the ground would probably have thought they were a couple of soft penalties. I'm not going to surprise you by saying I thought ours was a valid penalty and rightly given," said Hughes.
"My view on Cardiff's penalty is that it was very soft and the lad has actually looked for a movement from Steven N'Zonzi that would allow him to go down and I think he was always looking to go down in that situation.
"He drew the movement from Steven - (it was) very minimal, if any, contact and obviously difficult for (referee) Howard Webb when players go down in those situations. It's difficult to read whether it's a correct decision or not.
"That just came at a time in the game that was a little bit frenetic for us. It was probably the only time in the game where Cardiff got a little bit of momentum and created a few opportunities for themselves."
The draw keeps Stoke on track for a maiden top-half Premier League finish, in Hughes' first season at the club.
Although his side missed out on victory, the Stoke boss declared himself satisfied.
"I thought our control of the game was good again. Certainly towards the end of the second half I thought we were in the ascendancy and looked more likely to win the game," he added.
"In the end, we take a point. Given the circumstances at Cardiff and where they find themselves it was always going to be difficult.
"All in all, we're reasonably happy with the point we've got."
