Scientists not believing Mafune's story of a dinosaur in Japan seems silly at first, considering how kaiju attacks are taken as everyday occurrences in the '70s films, until you remember that his initial discovery of Titanosaurus took place fifteen years prior. People would still often react with "A giant monster? Surely you're joking!" well into the 1960s, especially considering that fifteen years would've made it 1960 - Major events like Mothra and King Kong vs. Godzilla hadn't even happened yet.
That, and considering Japan had already suffered the wrath of two Godzillas, two Rodans, Anguirus, and Varan (plus two Mogueras and their accompanying alien invaders), perhaps the scientific community were Properly Paranoid, and were in denial about the possibility of such events happening again.
What actually seemed to have gotten Dr. Mafune excommunicated from the scientific community was his claim that he could control Titanosaurus and by extension all of sea life. Imagine the kind of power Japan would possess — except this is the exact kind of scenario Dr. Serizawa feared if his Oxygen Destroyer device ever saw widespread use as a weapon. Perhaps their scorning of Dr. Mafune was the scientific community taking heed of Serizawa's fear and sacrifice.
