Plenty of cars do have religious symbols on or in them, e.g. crosses dangling from rearview mirrors, and that's more noticeable to a pedestrian than the eruv.
It's freedom of religion, not freedom from religion.
Except it's legal to park your car on public streets, as long as you follow the parking laws and limitations that are displayed. On the other hand, you can't throw whatever objects you want on public structures without a permit. They're not the same thing.
The eruv is also allowed by the city and thus legal.