Because probiotics can't be patented and pharmaceutical companies can't benefit financially from them. There are few studies of natural, alternative treatments because there are no huge companies willing to fund their research. Also, if there was a highly effective, natural treatment, millions of IBD patients wouldn't need their maintenance medications - resulting in a huge financial loss for both pharmceuticals and physicians.
The Centre for Digestive Diseases in Sydney, Australia is one clinic that has been studying and using probiotics - both orally and rectally - and has had much success. From their Web site:
Researchers at the Centre for Digestive Diseases have been trialing the use of living organisms to treat ulcerative colitis on the basis of restoring the balance of healthy bacteria in the bowel. Our results are at the forefront of world research in this field and may eventually provide a valuable alternative to the current immunosuppressant medications with the added benefit of no side effects.