Wanderers dominated the contest and were unlucky not to secure all three points when Stuart Holden struck the post in the 78th minute.
Johan Elmander was also denied on several occasions by Cottagers goalkeeper David Stockdale, who had been selected by Hughes ahead of Arsenal target Mark Schwarzer.
The Australian was facing a late fitness test ahead of the match due to a back problem but his absence from the squad may also have been explained by the fact that he had recently handed in a transfer request with a view to joining the Gunners.
It was the hosts who carved out the first opportunity after 10 minutes as Elmander attempted a flick, collected the rebound and then dragged a shot wide to Stockdale's right.
A minute later at the other end, Fulham skipper Danny Murphy went closer with a low strike from outside the box.
Wanderers debutant Martin Petrov, regarded by many as one of the most astute purchases of the summer after joining on a free from Manchester City, began to make his mark on the game and cut into the box incisively after being fed by Kevin Davies, only to be halted by a wonderfully-timed challenge by John Pantsil.
Gary Cahill connected with the corner which followed, but his downward header was comfortably collected by Stockdale and the centre-back leapt again in the box soon after but was unable to meet Petrov's inswinging free-kick.
Moments later, Petrov drove in a fierce effort which Stockdale had to dive to catch, before Bobby Zamora, looking confident after making his England debut in midweek, attempted an audacious lob that drifted just over Jussi Jaaskelainen's crossbar.
Having struggled to impose themselves, Fulham then enjoyed a spell of possession with Gretar Steinsson clearing a bouncing shot from Simon Davies and Zat Knight heading behind Damien Duff's free-kick.
But it was Bolton who continued to make the more legitimate chances, as Elmander dispossessed Dickson Etuhu and sent a powerful strike into the arms of Stockdale.
Jaaskelainen then got in a mix-up with Paul Robinson and fumbled his header, but the Finnish stopper dived on the ball before Zamora could capitalise.
Bolton were again the brighter side as the second half got under way, with Holden firing in an ambitious effort that rose off-target before Elmander collected Steinsson's cross in the box, swivelled and unleashed a snap-shot which Stockdale tipped over for a corner.
Having had a fairly quiet afternoon up until that point, referee Stuart Attwell was then heckled by the Bolton supporters after making a series of unpopular decisions.
First Elmander hit the deck after a collision with Brede Hangeland on the edge of the area, only for Attwell to wave play on.
The official then awarded Fulham a soft-looking free-kick when Fabrice Muamba made contact with Aaron Hughes, before ignoring the home crowd's cries for a penalty as Lee Chung-yong went down in the box under the challenge of Murphy.
Lee made a tame effort on goal moments later, but Elmander was unlucky not to score once more after working his way into a shooting position, with Stockdale on hand to avert the danger.
Zamora was the next person to show his displeasure with Attwell and received a booking after raising his hands to the official and appearing to grab his shirt.
Fulham were looking frustrated in general and Holden went closest to breaking the deadlock with just over 10 minutes to go, firing in a shot that bounced back off the post.
Bolton boss Owen Coyle made a treble substitution in the final minutes, bringing on Matthew Taylor, Mark Davies and Ivan Klasnic for Petrov, Muamba and Elmander, but the visitors stood firm to earn their manager his first point.