We do use "weren't", when it is in the past:
He asked me yesterday if I'd like a cup of coffee, and I replied that I would if it weren't too much trouble.
The difference is in the tense of the statement being made. If the response above was instead a direct quote, it would read like this:
He asked me yesterday if I'd like a cup of coffee, and I replied "I would if it isn't too much trouble."
The first case is a description of a past event, and uses the past tense; the second is in the present and uses the present tense.
Update:
However, if your question is about the use of the subjunctive as suggested in comments, then the phrasing would resemble this:
He asked me yesterday if I'd like a cup of coffee, and I replied "I would, if it weren't that my diet forbids caffeine."
Admittedly that last sentence is a bit contrived, but hopefully illustrates the difference.