Intuitive appeal is overrated. Aristotelian physics (motion derives from continuous application of force) was intuitive to a lot of people for a very long time. And then Galileo came along.
Not the best example, Galileo argued plenty from positions he saw as intuitive, even though he was completely wrong.
Also, according to the physics of the day, its completely understandable as to why they thought that way, intuition comes from observing nature, even if those observations may be incorrect simply from not being able to gather the data properly.
It's not about first impression intuition. I'll bet you'll find relativistic quantum field theory less intuitive, at the popular level, than either string theory or dark energy -- but it has more empirical support than almost anything else in physics.