I think you got it backwards. \$V_{in}\$ is controlling \$I_{B}\$ via Ohm's law (assuming the voltage drop on the base is small): \$I_{B} = V_{in}/ R_1\$. The BJT is in turn controlled by this current: \$I_C = \beta \cdot I_B\$.
In the end there is a linear relationship between \$V_{in}\$ and \$I_C\$, but this is only true for as long as \$R_1\$ remains constant. Since \$R_1\$ is not part of the BJT, you cannot assume anything about it when discussing BJT characteristics, and you cannot say the BJT is controlled by \$V_{in}\$.
Perhaps an example would explain it better. Imagine I drive a car, and its speed depends on how hard I push the gas and for how long. But I don't want to get any fines, so I always respect speed limits. Now you come along and say:
Why do they say cars are controlled by gas pedal, when in reality their speed depends on littleflat metal disksobjects with numbers painted on them?
So what you say is true in this particular case, but that doesn't change the fact that cars don't care in the slightest about disk-shapedflat metal objects in their surroundings.