A prejudice can be entirely rational--for instance, I am prejudiced against jumping into a crevasse because the outcome would be disadvantageous for my wellbeing.
Secondly, if the Vulcans are prejudiced against Spock, it is because they perceive his human DNA to predispose him against rational behavior. As far as I know (aside from the new movie), Vulcans never ganged up and poked fun at Spock. They simply view him differently.
Actually that is not entirely true. Reading between the lines Vulcans do actually have emotions. The Vulcans are really engaging in the sort of behaviour we read about in history towards mixed racial characteristics amongst humans- ie. African American, European for example. The fact is that while you are looking at the ideal, the truth is that most Vulcans do actually have emotions and act on those even if they lie to themselves about why they did what they did. The Vulcans do not like Spock because they see him as different. Vulcans especially being the logical, rational race would prefer the same type. It is kind of like the old phrase about "Why can't you be a non-conformist just like everyone else." While IDC is a concept the Vulcans bandy about, it is a concept that is not really honoured by their breaches of it. Even Spock's Father in the original series for a long while holds up these views.