There are a couple of ways to achieve this. You can use a genome browser such as GBrowse (http://gmod.org/wiki/GBrowse) or JBrowse which is capable of consuming a bam file and give a coverage display. GBrowse is a highly configurable genome browser and is useful for detailed visualization and analysis purposes. The tutorial at http://gmod.org/wiki/GBrowse_NGS_Tutorial shows how to do this in GBrowse. The downside of using GBrowse is that you have to install the software and learn how to configure your display. Also, you may not be able to get publishable quality images from GBrowse.

Alternatively, you can generate an abundance file and plot it using a tool like R. First, you need to obtain the start and end coordinates for the alignment for each read. Since these are RNASeq data, you have to discount introns from your alignment. You can achieve this by using the CIGAR string. Or, you can use the program bamToBed from bed tools to achieve this.

bamToBed -split -i input.bam > output.bed

The -split switch will take care of introns. From the resulting bed file you can generate the number of reads spanning each position by writing a simple perl or python script and plot the region of your choice using R. Hope this helps.

For a quick start have a look at SeqMonk http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/