It is true sometimes bosses have no idea and like you said if you don't look sick, sometimes people think you are hamming it up. Talking about what goes on while in the bathroom half the day is a tough subject to talk about with bosses/friends etc. (somewhat of a taboo subject unless you are a crohnie). If you have to give them a why give them a info on the illness and let them know they will never truly understand. Its impossible until you walk in these shoes. Reassure them you as best you can, but in the end you are at the mercy of the illness until they find a cure. You can also ask them if they prefer you stay at your desk after you have had an accident in you pants and see how they respond....ha ha.....I have been on the receiving end of similar situation. Got really sick this year, ended up needing surgery (ileostomy), got back to work and wouldn't you know it I was let go. This is the second time the same thing happened. Surgery in 2005 got back to work and shortly after returning got let go.
After a major surgery.........you need a lost job like a hole in the head.......
In the end you have to understand working for people who see you in this manner aren't people worth working for. Crohnies are what I believe as some of the toughest people out there. Remind your self how far you have come and how much you have accomplished in life and then remind yourself you did it while being unwell all the time. It doesn't pay your bills but it helps keeping you in the frame of mind where you wont get so down about the unfortunate reality of living with Crohns/Collitis/IBD. Stay Strong! Hope you get and stay well.