I'll bite. It is far harder to carry a baseball bat into a bathroom and beat someone to death than it is to have a knife in my pocket and shank someone. I am also going to go out on a limb here and suggest that carrying around a bat is also prohibited in school, however, one would be allowed on school premises because (shocker!) a baseball hat has a function deemed appropriate for school (even if baseball is pretty boring). A knife has no function that would require a student to have one.
The outrage also isn't over the fact that a 4" knife is considered a weapon. It is that a boy was found one to have it in his car (and therefore, his possession). If only the outrage was the same every criminal found with an illegal item / substance who claimed it wasn't theirs! This doesn't even have to be a knife. It could be a gun. Would the outrage be the same? Even if it "wasn't his"?
Common sense should tell you the school has rules barring all weapons from school, a knife is a weapon, a student was found with a weapon in his car and is then suspended. I think 90 days a bit much for alternative school (a friend of mine in high school was found with a shotgun shell in his car and only got 60 days in alternative school, but this was in Texas).