There are certain kinds of antibiotics that can affect your birth control, so lots of people have gotten pregnant on them because they reduced the effectiveness of their pills. Other than that, definitely an ongoing infection could throw off anything in your body (UTIs can cause pre-term labour late in pregnancy) including ovulation, so I wouldn't worry too much about the antibiotics doing too much. I'd rather be on antibiotics TTC than with a UTI (my husband definitely wouldn't even be allowed near me if I had a UTI!). Good luck!