What people are generally saying here is that 'females' as a noun tends to be associated with a derogatory attitude, not that every person who ever says it is a misogynist dinosaur.
I was thinking about it this morning, and I think for me the problem is that it uses one single facet to define a whole group of people, as though they didn't any longer have to be thought of as 'people' or 'customers' or 'employees', because their femaleness was the only thing that was important about defining them.
That's why I have a problem with it being used as a noun. I don't define myself primarily by my gender - I am a person, a parent, an employee, a customer, a reader, a viewer. I am a female person but I am not 'a female'.
I'm also not 'a white' or 'a middle aged' or 'an educated', though those are all adjectives that you might use when describing me.
The people who use this term may be doing it without thinking, because it's just not something they have considered. But others do it, deliberately or subconsciously, because it sums up their attitude to the whole female gender. That they are defined, and dismissed, because they are female, not considered as in any way equal or equivalent to men.