It was set up in order to reduce car use, and increase cycling to work, so even if you aren’t using the bike you bought to cycle to work, but are using another, I think you can have a clear conscience.
Also, alot of the bikes bought probably wouldn’t have been bought had it not been for the CTW scheme, therefore rather than costing the government/taxpayer money, we’re actually just helping the bike industry a bit more.
Most people I work with now cycle to work, I think the CTW scheme has helped.