In terms of protection, how does this automotive power supply circuit look?
First pass:


Your schematic is confusing. What is the relationship between JP1-1, VIN, BPOS and the battery voltage?
You should have the fuse on the positive input 'ahead' of your protection circuitry (on the battery-side of things). You never know how things may fail in real life. 

Given the orientation of D2, the battery feed should be JP1-1, correct? If so, and if you have reverse battery, your unidirectional TVS will conduct big current (it will indeed act like a diode) and melt things, and your PTC is powerless to help.

You may want to consider the bidirectional TVS 5.0SMDJ30CA (notice the extra C) so that it will clamp regardless of polarity.

If VIN is the battery feed, your circuit won't work as D2 will be blocking all the time.