I regularly travel with Westbahn, because they partner with Flixbus... their trains and the personnel are awesome (for what it's worth, they operate a smokers lounge on the train... a blessing for every smoker!).

The problem with Westbahn is that they're likely deep in debt and still not profitable (https://de.wikipedia.org/wiki/Westbahn_(Unternehmen)#Gesch.C...).

And for the Railjet: it's cheaper because the track fees are lower - here figures from 2011: http://www.drehscheibe-online.de/foren/read.php?3,5403272