I'm not asking the question on a superficial level. Obviously, (most) transcription factors are not acting directly on a substrate to produce a chemical change. I pose the above question as more of a philosophical inquiry.
First, a definition: A catalyst is a substance that increases the rate of a chemical reaction and is not consumed in the reaction. As every biochemistry class emphasizes, catalysts do not change the equilibrium constant of a reaction, only the rate.
So for example, if we take the following example of transcribing a gene of length $n$ ($G$) into a transcript of length $n$ ($M$).
$$ \ce{RNAP + G + nNTP <=>> RNAP + G + M} \mbox{ (Reaction I)} $$
The hydrolysis of the NTP's bonds drives the reaction forward (source). The Gibbs free energy has decreased. Obviously, there is some probability that the NTPs in solution would spontaneously polymerize into the length-n transcript, this possibility is unfathomably infinitesimal though.
The RNA polymerase is acting as an enzyme here, since it's 1) increasing the rate of an otherwise slow reaction and 2) not being consumed in the reaction. Our nomenclature is consistent as we usually reserve "-ase" suffix reserved for enzymes.
Transcription factors bind elsewhere on the DNA and facilitate (or impede) the formation of RNA polymerase complex from its constituent subunits ($mS$). Assume we have an activating transcription factor $TF$. We can model this as:
$$\ce{TF + mS <=> TF + RNAP} \mbox{ (Reaction II)}$$
Putting these reactions $I$ and $II$ together, you might have:
$$\ce{TF + mS + nNTP <=> TF + RNAP + M}$$
From our understanding of activating transcription factors, we know that this will increase the rate of the transcription reaction. The TF is not being consumed in the reaction. So, what am I missing here? Why isn't this transcription factor considered a catalyst for helping to stabilize the initiation complex?
