Houston was pleased with his side's display but they fell behind to a first-half brace from Ryan Stevenson, one goal coming from the spot, and, although Keith Watson pulled one back after the break, Houston's men could not get a leveller.
"I thought the team that played the better football lost today," said Houston.
"We played quite well in the first half as well and again it comes down to an individual error. Brian (McLean, defender) should deal with the first goal, but we didn't deal with it properly and we found ourselves a goal down.
"I haven't seen the penalty again. I thought it was a bit soft, but other people have told me it was a penalty kick.
"We found ourselves chasing the game and second half I thought we absolutely pummelled them.
"We were the away team today but we pinned Hearts back and they were desperately hanging on.
"They cleared everything we threw into the box but I'm walking away from here with nothing and I feel a wee bit hard done by. The ball didn't break for us today."
Former Hearts man Rudi Skacel was given a good reception by the home supporters and Houston was happy with his display.
"I thought he worked really hard," said Houston. "He's been playing really well recently and that's why he played. It was his shot that we got the goal from. I thought he worked his socks off but nothing really broke for him today."