I started doing pilates because of mild low back pain.  Many of my clients come to be because their doctor sent them.  I have one client whose doctor thinks pilates has been instrumental in keeping her out of back surgery.  Is it the pilates?  I don’t know, but do like to think pilates is helping. 
But a couple weeks ago a client told me that a friend’s doctor and physical therapist told them that pilates is bad for your back because pilates attempts to change the natural curves in the spine that people are supposed to have.  And I wanted to touch on this briefly.
First of all I want to say it is possible to hurt yourself doing pilates, just like it’s possible to injure yourself doing anything.  If you try an exercise that you aren’t ready for yet, you can get hurt.  If you don’t stabilize the pelvis when you move you can put more pressure on the back. If you fling the body up during the roll up or teaser and don’t move from a place of control you can hurt yourself.  But if you attempt to make good choices for your body and don’t try and push beyond a level your body is ready to work, I really think pilates is a great type of exercise for balance of muscles and overall health in the body.
There are also different styles of pilates.  I have taken classes where the entire class in done in a neutral pelvis.  I would argue that for the average pilates practitioner this would be unsafe and could put their back and risk. 
As to the comment that Pilates attempts to change the natural curve of the spine, I’m not entirely sure what is being referred to here.  I’m think this comment is assuming that pilates works in imprint all the time.  And maybe some styles of pilates do that.  I can’t speak for every certification program.  But I’m guessing that the individuals who said pilates attempts to change the natural curves of the spine are either not that familiar with pilates or had a bad training pilates program
That’s why in class we sometimes work in neutral and sometimes work in imprint.  The body requires a variety of movement.  And different bodies benefit more from different types of movement.  If you have a really tight low back, learning to imprint will be really good for your body.  Pilates isn’t trying to get your body to be permanently in imprint, but just capable of imprinting so that you can have full control of your movement and have a good range of motion.  If you have a body where you have a very weak low back, generally learning to be in neutral is going to be good for your body.
Pilates is about balance.  We ideally are working to restore the natural curve of the spine in everyone’s body.  To get there some people need to practice imprint more, others need to practice holding neutral more.    We really strive to get opposing muscles working equally and appropriately to try and hold the body in place.  We want stable bodies in pilates.  If someone has one muscle that is really tight and the opposing muscle is really long or weak, that person is potentially going to be in pain.  If you get those muscles working harmoniously and have neither pulling on the other, but balancing each other, you should be able to get someone out of pain.  Arguably if we could get all our joints into a neutral position all the time they should be pain free.  It’s when  a tight muscle or tendon is pulling something out of alignment that we have pain.  Given life, an imbalanced body is inevitable for all of us.  And pilates attempts to reach out to people for an hour a day, maybe an hour a week and help them find a more balance.
If you are in a group pilates class and all you to do is work in neutral or all you do is work in imprint or if you feel a bad strain in your body, question the class.  In pilates you should see variety.  Are there bad instructors and bad training programs out there?  Sure.  But if you find a good instructor and one who really understand the body, how it works and offers modifications, and if you listen and follow the modifications you need in your body, pilates can be a wonderful tool.  I truly believe that.  If I didn’t, I wouldn’t be teaching. 
And as a pilates instructor I’m a huge supporter of physical therapy.  I think people should go to physical therapy before they are injured.  It’s like any profession.  There are good doctors and bad doctors, good PT’s and bad PT’s, good pilates instructors and bad ones, good teachers and bad teachers.  Find a person who is good at whatever they do, and you’ll have something positive you can gain from them.