flu and pregnant?

I'm about 6 weeks pregnant, and I have the flu.. Doctor prescribed amoxicillin 500mg 3 times a day for 5 days and told me if it wasn't cleared up in 2 days to start taking it. I had a previous miscarriage and I'm worried this will effect it? Should I take them? Is it safe? I don't have a good relationship with my doctor and I don't trust him, he's the only doctor I can see. Help?