Is the only difference between Filipino and Tagalog the alphabet used to transcribe the various associated words?-Thanks.
Filipino is a standardized register/dialect of Tagalog language.
There exist other, non-standard, dialects of Tagalog. Each of those have differences to each other (e.g., if they were absolutely matching, they would be not considered different ones).
The Wikipedia article on Tagalog lists several important differences between the dialects of Tagalog language, including differences to the standard register (Filipino). This includes phonology (glottal stops and consonants), morphology (suffixes), and more.
Ethnologue states Tagalog as consisting of two branches, Filipino (fil) and Tagalog (tgl).
So "Tagalog" seems to be ambiguous (or rather underspecified), referring to both the more general and the more specific branch.