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A "site" in biology can mean several things.
First, it can mean the position of a nucleotide in a gene sequence or alignment. For example, you may have a single sequence and can see that at site 43 out of 650, there is an "A". You could also see that in a nucleotide alignment of two sequences, there is a single difference at site # 400. In the case of the alignment, the site # refers to every single nucleotide in the column of that alignment.
The other meaning for site is the more general one that you described wherein a "TATA" box is labeled as a "start site" for a gene. In thise case, the meaning is similar, you are still referring to a "position" or "site" along a gene sequence.
In short, site means a single position along a gene sequence or alignment.
