This is the type of fallacious reasoning I see quite often. The three best ways to score are layups/dunks, free throws, and threes. The Rockets shooting a ton of threes doesn't mean they can't get a lot of free throws also. Instead, they shoot a lot of threes and a lot of free throws by not shooting much from midrange.
Per Hoopdata, the percentage of shots that the Rockets take from different distances breaks down as:
39.0% at the rim (3rd in the league, average is 32.1%)
9.9% 3-9 feet (23rd in the league, average is 11.4%)
3.8% 10-15 feet (30th in the league, average is 7.9%)
13.1% 16-23 feet (30th in the league, average is 13.1%)
35.7% three pointers (2nd in the league, average is 25.0%)
Needless to say, you get most of your free throws on shots at the rim. The Thunder, however, lead the league in FT/FGA by a wide margin but only take 32.4% of their shots at the rim (13th in the league). It would be more interesting if Hoopdata included shooting fouls (where someone is actually fouled in the act of shooting, not just when their team is in the penalty); I'd imagine many of OC's free throws come on missed shots at the rim when they were fouled, therefore those wouldn't show up as FGA.