The rotation of the minecart is a bit inconsistent. So far as I tried its not possible to rotated an created minecart around the x-axis. However its possible to rotate a minecart briefly when summoned. A way to make constantly rotated minecarts now is to constantly destroy and summon new ones each tick.

Reproduction:
Using

\summon MinecartRideable ~ ~1 ~ {Rotation:[0f,45f]}

on an commandblock summons a Minecart that briefly is rotated and then turns horizontal again. However sometimes if you push it quickly before it has been reorientated it could hit a block below and stop reorienting and keep rotated.

Using

tp @e[type=MinecartRideable] ~ ~ ~ 90f 45f

will rotate around the y-axis but completely ignores the x-axis rotation (the 45f).

Using

\entitydata @e[type=MinecartRideable] {Rotation:[90f,45]}

shows the same behavior and only rotates around the y axis.