(1) They got guys who are better at attacking the rim than we do.
(2) Like you said, Boston is a small ball team itself. It evades the paint, plays on the perimeter and tries to attack from there. Some of the team's players have post games. Many do not (like Theis). Those who can post -- mostly Smart or one of the SFs -- Houston had guys who can matchup reasonably well against in the post.
At that point, is the post up option a better option than Boston's regular offense? I don't think so. Maybe the odd one here or there but not good enough to abandon the regular offense in favour of post ups. The regular offense was still Boston's most efficient option.
In summary, Boston (like many other teams) lack the personnel to truly exploit Houston's small ball lineups.
Everyone has been so focused on playing the perimeter game and so few players have truly developed their post games that very few teams out there are good enough at posting up to take advantage of Houston inside.
Boston had a better shot at beating them to rebounds than they did attacking them in post ups. Unfortunately, rebounding isn't well taught nowadays either.