A brief synopsis. Probiotics communicate with the immune system in a particular way, though it is not entirely clear all of what happens. It looks like they give signals to the regulatory T-cells to say "all is clear" and to assist in recognizing what is or is not harmful to our system. So it often helps people with autoimmune issues, like us. It also crowds out bad bacteria and can even act as an antibacterial to these other harmful microbes. They also keep in check the bacteria and yeast that are in the middle of being good and bad (good in that normal numbers some are anti-carcinigenic, etc. and bad in that in large numbers they wreak havoc on the body when entering the blood stream). They also aid greatly in digestion, which is probably why yogurt is better tolerated and has a lot of good stuff in it as a result. They break down fiber, opening up another energy source for our body to digest. They might even have healing properties, whether directly or indirectly by lining the walls of the intestines.
The benefits in the medical journals show that many attain remission and others show it just as affective it retaining remission as taking the standard 5-ASAs and I mean the results where so very near identical with a couple hundred people in participation. The question becomes which one(s). Some are better than others and have a better medical study backing them up.
As far as people not handling the probiotics so well, there is the chance that the body mistakes it for harmful bacteria. Usually it seems to be that the body is adjusting the balance of microflora and as the bad bacteria die off, it can cause an immune response, temporarily worsening symptoms before improving (i.e. herxheimer reaction). Also, if you tend to eat unhealthy (lots of sugar and refined flour), it is still feeding the bad bacteria and hindering the adjustment. With soluble fibers the probiotics thrive and even then gases are given off by them, but as you adjust, these gases are absorbed by other bacteria (this is what happen when I adjusted to eating much more fiber, such as beans and I actually did adjust after a few days). Also, it may help to either lower the dosage and you can even break open the capsule and pour it into food or drink that is slightly on the cool side or at room temp. The other problem might be the additives that placed in them that some may have allergies to.
Personally, this is the one thing I have been consistent with taking and I have seen significant improvement. I wish I could say it was single handly shown to be probiotics, but i tried a lot of stuff, but it seems to be the only thing that makes the most sense to show the benefits it has and changing my diet to what I am sensitive to and what best benefits my gut ecology. What do I take? Primal defense, florastor, probio, culturelle, yogurt, kefir, and cheeses... yum (BTW, I'm lactose intollerent as well) and I tried VSL3 for a couple months beforehand. I believe highly in variety being the best until better studies come out.