Methotrexate is an immuno suppressant so it has to slow down the immune system from producing things that are usually helpful in making the body heal. Sometimes however the immune system can actually compromise healing for instance inflammation.

Inflammation can 'over react' and make the problem much worse which is what you see in arthritis and skin conditions such as yours.

Anyway..methotrexate does have its side effects but in small doses once (maybe twice) a week it tend to be 'safe' especially for a person who isn't riddled with lots of other more serious health complications.

It sounds like you don't have many other options to help treat your condition as methotrexate is a last resort medication and isn't usual used as a first line of defense thing.

If you are really concerned enquire as to the dosage..maybe you can use it in conjunction with another medication?

Good luck

ETA: After reading Trillians post- yes definatley go to the doctors for a slip for blood tests. You may not require them for a long time though depending on how long your on it