Downtown La Crosse is relatively safe at night for a college town. The downtown area has several bars which cater to college age customers. As with any area populated by bars, you may encounter intoxicated and/or obnoxious individuals. Generally, you can negotiate this area without any significant problems. If you are looking to avoid the younger crowd, it is recommended that you avoid the downtown area after 10:00 pm.
There have been recent shootings (http://www.lacrossetribun...) in the area, but these are fairly isolated. Also, recent reports that drownings are actually criminal acts (http://www.fox25fox48.com...) have been debunked by, among others, the FBI (http://www.wjla.com/news/...)