Both of those matter. Cleary low latency is good but if you can only service a few users every minute then your throughput is low and the site doesn't perform well for a large number of users.
Some evidence to show the importance of latency to companies revenues.
According to research conducted by google in 2009, after artificially introducing 400ms delay to search response, 0.74% searches are performed by users in next 4-6 weeks. Another research about Bing suggests that a 500ms delay would lead to loss of 1.2% revenue per user.
I feel like the relative importance of latency and throughput is dependent on the purpose of the website, the size of its user base, etc. For example, a site might serve a super specific purpose important to and used by a very small number of people - in this case, the latency would presumably be much more important than throughput. However, for a site like Facebook, which has a HUGE user base, high throughput is as, if not more, important as low latency.
Two good papers to read on this topic: