TL;DR: You're not imagining the boys' attitude in the title sequence, even though they don't demonstrate a similar attitude in the series.
In most of the actual episodes, Phineas and Ferb appear to want (genuinely) to please Candace. However, the title sequence was conceived and largely animated before the regular run of the show: the "pitch" for the show consisted of a story-boarded version of the first episode, complete with title sequence and theme song. While the show in the pitch is very recognizable, some elements did change over the course of the show, including, notably, Phineas and Ferb's attitude towards Candace.
From the lyrics to the theme song:
Finding a dodo bird,
painting a continent,
or driving your sister insane!
[Candace:] "Phineas!"
In that last pair of lines, Phineas appears to be painting a mustache on a portrait of Candace, which turns out to actually be Candace. The pitch lyrics also includes a muttered "aside" from Phineas1:
or driving your sister insane!
[Phineas, muttered aside:] "It's a short drive."
[Candace:] "Phineas!"
Painting a mustache on Candace, whether they believed it was a portrait or knew it was really her, is a much more hostile act towards Candace than we see in actual episodes of the show, and the lyrics suggest that Phineas might have one day announced "Ferb, I know what we're going to do today! Drive our sister insane!" Later in the storyboarded pitch (about 6 seconds into part 3), Ferb also has a line about the possibility that Candace might be put in charge which at least suggests that he doesn't like the idea.
It thus appears that there was originally a plan for two-way animosity between the boys and their sister, but this was abandoned (along with the name Dr. Meddleschmidt and the gag of Candace being in charge "conditionally", which made it into the pilot but not later episodes) for the rest of the show. However, unlike Meddleschmidt and the bawdier script elements, some vestiges of the idea remain in the title sequence.
1 Phineas has these asides throughout the title sequence, most of which did not make it into the final version of the song; one exception is "Locating Frankenstein's Brain/[Phineas:] 'It's over here!'"