Skeleton can ride boat but can't shoot the player, his animation's would be transferring from the normal passive form to its aggressive.
Related issues
is duplicated by
Comments
Also affect Witch, Blaze, Guardian.

Confirmed.

Confirmed for 16w05a.
Another thing to add to this issue which makes it very strange; Skeletons appear to not be able to shoot while in boats, however they are able to shoot while they're riding other entities. Very strange, but it's really good to know there is a fix currently.
Also affect Snowman.
Confirmed for 1.9-pre2

MC-96588 may be equally related

Confirmed for 1.9.
Confirmed for 16w15a
Confirmed for 16w15b
Confirmed for 1.9.3-pre1

Changed reporter to @unknown as the reported doesn't update affected versions.

Still an issue in 16w21a for snowmen. They attempt to shoot snowballs but end up hitting only themselves. Blaze and other mobs appear to be working though. Might have to do with the position of the snowball when snowmen first throw it. This should be reopened or perhaps a new ticket created as the issue is only snowmen and has a different cause now.
@Jeremy that's another issue.
Link: MC-88491

@les3awe Thanks.

So now the mobs can shoot out of the carts, but can you as a user, throw snowballs at pigmen (for example) while riding a minecart ? Has that been solved by this as well? Inquiring minds want to know

Yes.

Fantastic, thank you. Will this one make it into the 1.9 tree ? (I probably should have asked that at the same time)

Unlikely.
Can confirm.