So the reason Phineas is the actual protagonist of the show is because there's actually considerably more focus on him than Ferb. Phineas is clearly the leader of their group and the idea guy, while Ferb is mainly just an engineer. A big part of this is the fact that Ferb doesn't talk much, which causes the focus to immediately shift towards Phineas and away from Ferb. There are also some minor details. Notice how whenever Candace angrily stomps up to them and demands to know what they're doing, she ends up mainly talking to Phineas, since he's usually the only one who responds. In fact, most people (aside from Phineas) don't even directly talk to Ferb unless he initiates the conversation. Also take note of how Phineas has three different catchphrases used in every episode, while Ferb is mostly silent, making Phineas a more dominant character. Overall, Phineas is the most important character in the A-plot, and Ferb mainly exists to give him someone to talk to (hence his silence).