When professionally installed the 3M vinyl protectant (clear bra) will not harm the paint.
Unless you try to remove it without soaking it with isopropyl alchohol. It can remove the paint if you do - saw it happen! They were going to repaint the car anyway so they just tried to heat the vinyl a bit and pull it off. The paint came with it, so it sticks well to the car until you want it off and do it the correct way.
The strap-on bras will scuff and scratch the paint every time. Some dust or sand gets in behind it and the wind or vibration makes the bra move over the paint, scuffing it.
The clear vinyl comes in various thickness products. A nice thick one is used for headlamp assys. Expect to pay $200 to $300 for the clear bra, depending on how many pieces there are (side mirrors, how much of the front is covered, etc). Expect to pay around $50 for the headlamp protection - if it saves one headlamp assy it pays for itself four times over! I have both on my Pathfinder (the anti-Prius), and have watched a large rock bounce off the headlamp without damaging it. Ditto for the hood - though a sharp rock will cut the vinyl. This has happened three times on my RX-7. No damage to the paint, but the vinyl has small tears in it. There is also an insect here in Alberta that has non-OSHA approaved "guts". It will stain the vinyl a reddish brown and I haven't been able to get the colour out.
Bottom line though, is if the vinyl is damaged enough you want it gone, it can easily be removed (by the professionals) and replaced if you like.
Another tip is Zaino (search for Zaino Brothers). This stuff ("show car polish") is amazing. It takes a little work to "do up" the car properly but it's worth it, both for the shine and the protection. When I "Zainoed" (it's so good the car fanatics have made it a verb) my vehicles I found when finishing a highway trip, the coating of bugs can be removed by a garden hose for the most part.
First a word of advice. Any time you touch the paint you put minute scratches in it. You usually can't see them as they are usually very small. As you will be putting scratches in the paint, you want to make sure they are mimimally visible - so on horizontal surfaces move cleaning/polishing front to back/back to front. On vertical surfaces move up down/down up. This way the scratches will only show up at two angles, and they will look "normal". Never move in circles - this will leave "swirl marks" which will show up at any angle.
Zainoing:
1. Remove all wax from car - wash with "Dawn" dish detergent to do this - don't use dish detergent very often, once a year at most. It's hard on the paint.
2. Apply Z1 to prepare the surface. This can be done in full sun with no problem (other than you might overheat). Use as little as possible to just cover the surface.
3. Once the Z1 dries apply either Z3 or Z5 right over it. Z3 is the show car polish, Z5 is used if you have "swirl marks" from over aggresive polishing. Again, in full sun is no problem. Again, use as little as possible to just cover the surface.
4. Once the Z3/5 dries, wipe off the excess with a cotton towel. It wipes off easilly, just be gentle. You can leave it on for as long as you like before removing it. It will not "stick" or make a mess.
5. To finish, spray a small area with Z6 and quickly wipe off. Don't let it dry on the surface. It spreads the molecules of the Z3/Z5 to give an enhanced shine by making a "flatter" surface reflector. It also removes excess product that dims the shine.
6. You are now ready to apply another layer of Z3/Z5 if you like. Go to step 3.
The more layers you apply the "deeper" the shine. There are, of course, diminishing returns. I use 3 layers on my RX-7, and one or two on the anti-Prius as it's a lot of work on that vehicle (large surface area).
Step back and enjoy the shine! Check out most of the sports car forums for rave reviews of this product. You don't need a lot of it, either.
My tip of the day for this topic.