The result leaves their last-16 tie finely poised ahead of the return leg in Manchester on March 15 and United may feel concerned by their failure to create any clear-cut chances of note at Stade Velodrome.
The low-quality fare on show at the home of the French champions Wednesday was in stark contrast to the performances produced by United's Premier League counterparts Arsenal and Tottenham in their respective last 16 first-leg ties.
Spurs, Champions League debutants, executed a masterful smash-and-grab to beat AC Milan 1-0 in the San Siro, while Arsenal came from behind to defeat the all-conquering Barcelona 2-1 in a thrilling game in north London.
Chelsea also have one foot in the last eight following a 2-0 win at FC Copenhagen on Tuesday and Rooney sympathised with any fans who had tuned in with high hopes to watch United tackle Marseille.
"I can imagine!" he said, when told by journalists that the match had not made scintillating viewing for armchair fans.
"I watched both of those (Tottenham and Arsenal) games. They were great games and it's great to see Tottenham doing well in Europe."
Despite the disappointing nature of Wednesday's draw, Rooney said the onus was not on United to produce an all-out attacking performance in the second leg.
"I hope we do, but we'll just look to get the win," he said.
"At this stage of the competition, the win is the most important thing, however you do it."
In the absence of the injured Ryan Giggs, Rooney was asked to reprise the left-wing role he adopted during United's run to the final in the 2008-09 competition.
It was a task he performed with diligence, although his coach, Sir Alex Ferguson, admitted he was "better through the middle" after United shifted to a 4-4-2 late in the game.
"Obviously, when you're played out wide it is quite difficult to adjust if you haven't played there for a while but we've got injuries at the moment so if I have to do that, there's no problem with that," said the England striker.
One plus point for United in the draw with Marseille was the performance of 21-year-old defender Chris Smalling, who excelled alongside Nemanja Vidic in the middle of the United back four.
A summer signing from Fulham, Smalling was playing in his very first Champions League knockout game and admitted that it was an experience that would stay with him.
"Coming to Marseille, we knew what the stadium was going to be like and the other players had spoken about the atmosphere and said it was a great joy to be able to go out there and relish an opportunity like that," Smalling told AFP.
"A lot of my games this season have been at Old Trafford but to come here -- it's rare that you go out for the warm-up and you've got 90 percent of the fans already booing.
"It's great. Once you go in for the challenges and you've got the fans on your back, they're moments you relish in stadiums like these."
A 1-0 win for Arsenal against Stoke on Wednesday cut United's lead at the top of the Premier League to just a single point.
Ferguson's team now face Wigan, Chelsea and Liverpool in the league and an FA Cup tie with either Arsenal or Leyton Orient before the second leg against Marseille, and Rooney says it is vital the players keep their concentration.
"There are three massive games for us coming up now -- Wigan, Chelsea and Liverpool, and then maybe Arsenal after that in the cup," he said.
"It's a massive time for us in the season and we'll have to keep going and trying to create chances in those games.
"If we can get through those games, with a good amount of points, I'm sure we'll be up there."
Rooney remorse as United fail to match Prem rivals
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