Schalke were floored as Porto netted two second-half goals in quick succession, as Brazilian defender Eder Militao struck in the 52nd minute and Jesus Corona three minutes later. Moussa Marega hit a third late for the hosts in added time.
"You always have the right to express resentment, but we have qualified for the last 16 - I just don't get it," he said.
The mood of the disgruntled fans was made worse as the team did not acknowledge the travelling support after the final whistle.
"One could have gone to thank them in the stands, that is all about respect."
Schalke's injury-hit attack failed to manage a single shot on goal in the opening 45 minutes while Porto ripped the Royal Blues defence apart after the break.
However, Schalke deserve some sympathy in the face of a crippling injury list with five forwards injured.
Mark Uth, Breel Embolo and Cedric Teuchert are all sidelined long term.
"I have never heard of a Bundesliga team having five forwards injured at the same time," grumbled Heidel, who hopes to have Burgstaller and Skrzybski back from injury before Saturday's away match at Hoffenheim.
Schalke have lost only one of their five games so far in Europe, but are just four points clear of the bottom three in the Bundesliga after seven defeats in 12 games.
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