I've revised your post to a question, as it is not a tool post. Also, Bowtie2 is not a good tool for RNA-seq since it is not splice-aware.

You can filter out unmapped reads from the sam file after the fact, and convert the filtered reads to fastq, with BBMap's reformat.sh:

reformat.sh in=reads.sam out=mapped.sam mappedonly
reformat.sh in=reads.sam out=unmapped.fq unmappedonly

Or use BBMap in the first place (which is splice aware) like this:

bbmap.sh in=reads.fq outm=mapped.sam outu=unmapped.fq ref=ref.fa maxindel=200k