It's the great dilemma of the new wave of internet media and streaming. The full debate is way too long, and involves a multitude of things (read up on everything involving Spotify to get an idea) but it essentially boils down to "How do you monetise streaming video?" . Crunchyroll uses two approaches, premium subscription video, and ad-supported free streaming. I'm not certain of the exact details, but companies will pay them (or the advert delivery service they use) to place their ads. Naturally the more eyeballs there are per ads, the more Crunchyroll gets paid in theory. Thus they can support free streaming of their shows.
Of course, lately advertising on the net has been getting more aggressive. As Commissioner Gordon puts it at the end of Batman Begins, it's all about "escalation". They use pop-ups, we respond with pop-up blockers. They launch resource-hogging video ads wrapped around websites, we use Adblock. I'm not sure there'll ever be a solution. Personally, I lost my patience for horrible video ads last year when they really started slowing down my computer. I've had a few dodgy adverts try and put malware on my laptop too, so now I use Adblock on the most egregious offenders (looking at you Eurogamer!).
But yeah, the adverts are there on Crunchyroll for a reason. Personally, I prefer the subscription based model, which is why I like Netflix and Crunchyroll's subscription service.
