There was something of an anti-SITPWG backlash that year with the Tonys. SITPWG was seen as the show for snobs and intellectuals and, significantly, had been the subject of article after article in the Times by Frank Rich (then, the most hated man on Broadway) extolling its genius and indirectly (and sometimes directly) putting down "La Cage," Jerry Herman and the old-school Broadway musical with its "hummable" melodies. Rich single-handedly went out of his way to prop up the show which struggled at the box office. Rich's cheerleading (and the Pulitzer) helped keep the show running for well over a year, but engendered a lot of resentment around Broadway.
All of those bad feelings resulted in a a near shut out Tony night for SITPWG, which was viewed as not so much a snub of Sondheim (who has always been well-respected), but more as a slap at Frank Rich and the power of the Times which many felt had gotten completely out of control. It also didn't hurt that Herman and Fierstein were very popular figures in Broadway circles. And there was also the fact that "La Cage," despite its gay subject matter, was more audience-friendly and would be the bigger hit (which ultimately was the case).
So while Hearn and Chita Rivera (the first win of her long and legendary career) were certainly very deserving, Patinkin and Peters probably never had a chance at the Tony that year because of all the anti-Times, anti-Rich, anti-SITPWG sentiment at the time.
"What a story........ everything but the bloodhounds snappin' at her rear end." -- Birdie
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"The Devil Be Hittin' Me" -- Whitney