Phlox is not attacked on earth until the third episode, Home. That is the set up for the mass xenophobia we see on earth in the last part of the season. The NX-01 spends the majority of the season in deep space, which is the reason we don't see what is going on, on earth. But we begin to find out later in the season.The "wave" of bigotry though seemed to be in the season opener 4 when Phlox is attacked and then you don't see it really pop up again until the last few episodes at the end of the season.
Ask yourself one question (on this topic), did any of the spinoffs show mass xenophobic racism on earth, other than Ent? The answer to that question, regardless of all the superfluous, unrelated stuff you have brought up, is no.I mean I am not disagreeing that this stuff wasn't their. Only it just didn't feel so ant-classic Trek to a point where it didn't feel like they were doing things that Trek never dared to tackle before. It felt like Berman Trek with a extra layer.
Here's something else for you to stew on, Ent was the first Trek series to build an entire season on a single mission. That would be the Xindi mission in season 3.