I work in the centre for inflammation research at Edinburgh University. Your question is a really good one! And the answer is that inflammation reactions are essential but there is a trade off between the body healing itself in the short term and the long term damage it can cause. One example is an alcoholic who damages his liver - inflammation in the liver is a normal reaction to alcohol consumption except an alcoholic does this everyday so his liver is constantly inflamed and this is a problem. Similarly, people who suffer from coeliac disease have an immune response to gluten molecule (immune system incorrectly sees them as pathogens) which causes damaging long term inflammation to the gut.