Alexey, m2e-wtp needs to put /target/m2e-wtp/web-resources first as this folder potentially contains filtered (in the maven way) files, existing in src/main/webapp (think web.xml) and WTP always deploys the first file found. Changing the order is a no-go.
WTP 3.2.5/3.3.1 (https://bugs.eclipse.org/bugs/show_bug.cgi?id=353834) added a new tag="defaultRootSource" to virtual folders which should - hopefully - fix this issue. This fix has already been implemented in m2e-wtp 0.14.0 https://issues.sonatype.org/browse/MECLIPSEWTP-168.
m2e-wtp 0.14.0 should be released at about the same time as Indigo SR1, by the end of september 2011. If you can't wait to get your hands on this killer combo, you can get the pre-release versions :
Indigo SR1-RC3 : http://www.eclipse.org/downloads/index-developer.php
m2e-wtp 0.14.0-SNAPSHOT : http://download.jboss.org/jbosstools/builds/staging/m2eclipse-wtp-e37/all/repo/