I'd lay a lot of the blame on the source material. Percy Jackson reeks of trying to be an Americanised Harry Potter. The character archetypes are the same - main lead knows nothing of his origins, female best friend is a 'little miss perfect', male best friend doubles as comedy relief. They get sent to a secret school/training academy to use their abilities and uncover a secret plot on the part of the unexpected villain to gain power. Yawn.
Audiences aren't as stupid as studios think they are, and I think those comparisons were apparent enough to put people off. Sure, Lightning Thief threw in the whole road trip angle but the small differences didn't outweigh the enormous similarities.
That's not to say that Harry Potter is swellingly original - it's not. The Olympian stuff just seems to directly riff on that particular franchise uncomfortably closely though.