The Bible isn't against pelicans, per se. Pelicans are just large waterfowl with a long beak and a flexible throat pouch that can hold a lot of water and fish. They're really quite beautiful when they're not trying to steal your 26-dollar shrimp sandwich on the wharf.
The confusion came about because of Rudolf Bultmann. Bultmann was a biblical scholar who was a little too influenced by the Enlightenment. The Enlightenment was a time of great scientific exploration and discovery that decided anything that couldn't be explained by science must not be true. One of the results was a rejection of the infallibility of the Bible. Poetic passages were taken too literally, like that the earth was flat, and Scripture was spiritualized—meaning, if a literal interpretation didn't immediately seem true, it was deemed to be a spiritual metaphor. Or, even worse, in error.
Bultmann took this to an unhealthy level when he "demythologized" the New Testament. He basically believed that God did not directly interact with His creation, so any occurrence which claimed or insinuated a miracle must be a descriptive account of the primitive, uneducated, first-century writers. In order to properly interpret the writing, we must take away the magical elements and understand what the story means
to us.
To that end, Bultmann rewrote the anecdote about how Jesus fed the five thousand (Matthew 14:13-21). In the original account, Jesus has been speaking to a large crowd of people who grow increasingly hungry. The disciples scrounge up five loaves of bread and two fish. Jesus prays and the disciples pass out the food. To everyone's amazement, the entire crowd leaves filled, and the disciples collect twelve basketfuls of leftovers.
As Bultmann didn't believe in miracles, he proposed an alternate interpretation. He claimed "loaves" would better be translated "giant wagon trains," meaning, Jesus pre-arranged five competing bread merchants to stop by and finished His teaching when he saw them approach. The appearance of enough fish, however, was a coincidence. It so happened that a large flock of pelicans smelled the bread and, throat-pouches filled to overflowing, soared over the crowd. A small boy threw rocks at the birds, and they dropped their fishy cargo on the hungry masses.
Charles Ryrie, who believed the Bible to be infallible, strongly disagreed with Bultmann. There is no indication in Scripture that Jesus was aided by pelicans—God the Son was perfectly capable of turning two fish into several thousand. Ryrie had serious concerns about how Bultmann's interpretations of Scripture impacted his spiritual state. "Still," Ryrie was heard saying, "if God can save a
publican, he can save Bultmann."