It does not say .com names are $3.99
It is slightly misleading (since the default search box is for .com), but all it says is "DOMAINS FROM 3.99"
which is absolutely true. Some .info domains go for as low as $3.99
That is nowhere near as bad as GoDaddy's upselling crap PLUS namecheap's configuration and control panels are really nice to use.
Comparing GoDaddy to NameCheap is like comparing MySpace (before the last major redesign) to Facebook. They both have to make money somehow (and so have certain lame tactics to be competitive), but NameCheap is obviously lightyears beyond godaddy in any informed persons mind (ESPECIALLY when actually using the service after having paid for it... NameCheap's control panels are the best i've ever seen anywhere)