The ball will come towards you while the bus accelerates, because being in the air, it is not linked to anything, therefore, the bus cannot transmit its growing kinetic energy to it. Therefore, the ball will tend to oppose to the bus' movement and will seem to be going backwards, relative to a bus passenger's point of view. So it's all about point of views, which is the common term for reference frame :
When in uniform linear motion relative to an inertial reference frame, the bus is itself an inertial reference frame. Therefore, if you throw a ball with an vertical initial velocity, it will go up to a maximum altitude and fall in free fall like it was "on earth". Following newton's second law of motion :
$$
\sum{\vec{F_i}} = m.\vec{a}
$$
With $m$ being the ball's mass, $\vec{a}$ its acceleration relative to the bus reference and $\sum{\vec{F_i}}$ the sum of all forces applied to the ball, which in case of a free fall is reduced to the gravitational force only : $\sum{\vec{F_i}} = m\vec{g}$
Now, if the bus is now accelerating (relative to the earth's inertial reference frame), it becomes a non-inertial reference frame, which is way more fun because now, the second law of motion has inertial parameters :
$$
m.\vec{a} = \left(\sum{\vec{F_i}}\right) + \vec{F_e} + \vec{F_c}
$$
With $\vec{F_c} = -m.\vec{a_c}$ being the Coriolis effect, which in case of an accelerating bus is non-existent.
However, $\vec{F_e} = m.\vec{a_e}$ is more important here, because that's the mathematical model of "why is the ball likely to hit me in the face while the bus is accelerating". $F_e$ is called a fictious force, because it's a force that does not come from any physical phenomenon, but is used to make the second motion law model working in non-inertial frames, compensating for the non-inertial frame acceleration. It is equal to the object's mass ($m$) times the non-inertial frame's acceleration relative to an inertial frame. Let's say the bus has a constant acceleration of $\vec{a_b}$, the second law of motion applied to the ball in free fall is now :
$$
m.\vec{a} = m.\vec{g} - m.\vec{a_b}
$$
Or :
$$
\vec{a} = \vec{g} - \vec{a_b}
$$
Which translates in : while the ball is accelerated by gravitation, it also accelerates in the same amount of the bus, but in the opposition direction.