Peak-calling using homer
You just need to strip the / from $d, for which there are a number of options:

for d in */ ; do 
    dname=`basename $d`
    findPeaks $d -style factor -o ${dname}.txt
done


or

for d in */ ; do
    dname=${d%%/}
    findPeaks $d -style factor -o ${dname}.txt
done


There are likely other ways one could go about this. Having said that, since you're not running these in parallel you could simply move the default output file (peak.txt) to a file name of your choice (using one of the strategies above).