When I heard Christian Bale and Michael Caine both had roles in The Prestige, I immediatley made the Batman and Alfred connection.
When I heard Hugh Jackman was also in it, my first thought was "Batman vs. Wolverine". I know if I ever see, perhaps, Val Kilmer and Christian Bale in a movie together (i'd like them for Ozymandias and Dr. Manhattan in a Watchmen film), i'd immediately think of the fact that they were both Batmen.
The fact is, when two actors who either acted together before, or played similar roles come together, the connection is made. The general public will without a doubt notice the fact that the Brokeback Mountain stars are reuniting in the Batman movie, and countless jokes will be made. When the two characters interact, it will enter peoples minds that they once saw these two characters making out in a film, and they'll make jokes. It's as simple as that.
Personally, I wouldn't care at all, although I dont like Gyllenhaal for the role in the first place. The connection wouldn't bother me, but the fact that others will make lame comments does. If i'm watching the movie in the theater, see these characters together, and hear some idiot make a Brokeback Mountain joke, it'll greatly upset me.