The League Two side produced a battling display, but two goals - a poacher's effort from Daniel Muñoz and a classy finish from Justin Devenny - either side of half-time were enough for Palace.
Hughes, who claimed the broadcaster Player of the Match award, was crucial to the one real high quality moment in the game, picking out Devenny with a superb pass that split the Doncaster defence. The young Northern Ireland international did the rest, with a cool finish in front of the travelling support to put Palace in control of the tie.
The Eagles will now face another EFL side in the next round of the FA Cup, when South London neighbours Millwall visit Selhurst Park. And Hughes is full of belief that the group has the ability to go far in the competition.
"With the squad we've got and how seriously we take it, I think we've always got a chance," Hughes told BBC Sport.
"You know, the gaffer has told us that many times. We've taken all the cup competitions seriously with the team selections and how we approach all the games, so I think that's shown this season - so it's another chance to go far.
"The style we play really suits me. We've got such a good group here, a great squad. It was good to see a couple of faces back tonight, Matheus [França] and Adam [Wharton], who have been out for quite a while, so yeah, it was a good night all-round.
"I know it's a cliché, but we knew it was going to be a tough game. You look at the results over the weekend, although there weren't many shocks as such, all the games involving Premier League teams were really tight.
"I think it was really important to get the first goal and, of course, you've got to see it out at the end."