Fulham put themselves on course to break their 13-month winless away streak just after the half hour when Clint Dempsey came back to haunt Hammers goalkeeper Robert Green with the Cottagers' opener. Moments earlier, Hughes was livid that Marriner did not award the away side a penalty after Eddie Johnson went down in the box under pressure from Lars Jacobsen.
"I am disappointed we didn't get the awarding of the penalty because at 2-0 going into half-time it would have been difficult for them to come back," said Hughes, who saw his side denied victory thanks to Frederic Piquionne's second half header.
"Eddie got in behind the defence and if there is any contact whatsoever then more often than not it is a penalty.
"Unfortunately for us for whatever reason it wasn't given. From our point of view it was clear, there was a coming together, a tangle of legs and a goalscoring opportunity was denied, so it should have been a penalty."
The result meant West Ham stretched their unbeaten run to four matches but wins for Everton and Wigan meant the Hammers sank to the foot of the Barclays Premier League table.
West Ham manager Avram Grant was determined to take the positives from the result despite his side's current predicament.
He said: "They dominated the first half but after half-time we changed the shape, we scored and could have scored more.
"I think the most important thing today was first to take points and second to show that we are improving.
"The position in the league now is not important because one win can take you up four or five places. Fulham are having a good season and are playing with confidence and we are only four points away from them."