(0) Download the release and unzip it.
(1) Go the the directory where you find matsim-0.4.1.jar .
(2) Then type
java -Xmx2000m -cp matsim-0.4.1.jar org.matsim.run.Controler examples/tutorial/config/example5-config.xml
This should produce a new output directory. Meaning of the parameters:
-Xmx2000m : Increases the Java heap space to 2000MB of memory. If you have less memory, try smaller values, but the Java default is too small.-cp matsim-0.4.1.jar : The jar file (Java library) which contains MATSim.org.matsim.run.Controler : The class where the main method for running "iterations" resides. examples/tutorial/config/example5-config.xml : The xml file that contains all of the configuration of the run. The file can be edited.org.matsim.run.Controler" line again, you first need to erase some contents of the output directory.(3) Next type
java -Xmx2000m -Djava.library.path=libs/jogl-1.1.1/jogl-1.1.1-<your-os>/lib -cp matsim-0.4.1.jar org.matsim.run.OTFVis output/example5/ITERS/it.0/0.otfvis.mviMeaning of the parameters:
org.matsim.run.OTFVis : The class where the main class for the visualization resides.-Djava.library.path=libs/jogl-1.1.1/jogl-1.1.1-<your-os>/lib/ : OTFVis needs an additional library (see here). Please replace <your-os> with the version required for your platform.output/example5/ITERS/it.0/0.otfvis.mvi : The mvi ("movie") file that contains the simulation run in a form which can be displyed by the visualizer.This should produce a visualizer window that looks as follows:

(4) The logfile, with the above example in output/example5/contains, between a lot of other information, also a dump of a the full matsim configuration. If there are interesting parameters, you could try to copy then into your own config file, modify them, and re-run.logfile.log
In my (kn's) view, one can actually get quite far in this way, i.e. by just editing the config file. The main problem is how to obtain the network and in particular the so-called initial demand for your own scenario. If you can't get that from somewhere else, it is probably better to go through the "Learning MATSim in 8 Lessons" tutorial.