So freshman year I took honors algebra 1 instead of geometry like the majority. Does it count against me when applying to colleges that I took a lower course than the other students?
By the time you apply to college you will be submitting a whole portfolio of things: the rigor of the classes you took, the marks you got in them, your test scores, your ECs, the way the adults in your world evaluate you, and what you have to say for yourself. Which math you took in grade 9- esp given that you were in an honors level math, regardless of the topic- will not be why you do - or do not- get into any particular college. It’s where you go from where you start that will matter.
(also, the order in which math is taught varies a lot by school- algebra in grade 9 is a very normal thing overall, even if it isn’t in your school)
Some top schools (Wesleyan comes to mind) bragh about the percentage of their admits who took calculus. You will be at a disadvantage at those schools. Also often, but not always, math SAT scores for people who take Algebra 1 freshman year are lower than those who take geometry.
That said, plenty of people in your situation get into great colleges so all is not lost. Make sure to do ok in math but focus on the things you love to do and things will turn out ok.