Are anime episodes/manga chapters really free? I believe almost all of the people watching anime or reading manga get them from various sites like watchop.com, Crunchyroll, anime44, etc., and similarly for manga there are various sites. But are these episodes/chapters really free of cost for the audience? I know that these companies have their major source of income from merchandise and all other stuff but the episodes/chapters are available on net so easily that too for free. Aren't there any copyright violations? If there are why don't these anime/manga companies do something about it?
Yes, there are some legitimate websites on which you can read manga and watch anime for free. Crunchyroll is one of them. While Crunchyroll started out as a site that streamed anime without licenses (i.e. illegally), they are now fully legitimate and above-board. 

Of course, Crunchyroll has to pay for licenses for the anime they stream - the producers over in Japan aren't just going to give it away for free. So how does Crunchyroll make money? I don't claim to know Crunchyroll's business model, but (as this article points out), they have venture funding, and they sell premium memberships, as well as anime-related merchandise. They also show ads to non-members. Lots of websites follow a business model in which users get lots of functionality for free - for example, this one! 


  Aren't there any copyright violations? 


The other sites you mention - "watchop.com" and "anime44.com" do not appear to be licensed purveyors of anime, so in their case, yes - they are probably infringing on the copyright of the owners over in Japan. They presumably aren't paying the licensors in Japan a dime, so it's not surprising that they can (illegally) show anime for free. You probably shouldn't use those sites.


  If there are why don't these anime/manga companies do something about it?


Allow me to quote from Logan's answer over here (emphasis added):


  I'll also point out that while fansubbers and scanalators are almost certainly legally in the wrong, the number of cases related to this is quite small. There are several reasons for this. For one, the Japanese industry is built to sell merchandise in Japan, so they have little interest in prosecuting cases overseas. The licensing industry, on the other hand, was built around an already extant culture of fansubbing, and so they've always just factored that in.


Also, if I'm remembering correctly (and please, do correct me if I'm wrong; I'll try to dig up sources for this later), anime licensing deals are typically a flat fee - the licensees outside Japan pay the licensors in Japan a fixed amount in exchange for the right to stream the anime, or sell physical copies, or whatever. 

What this means is that the licensors don't care how many times the anime is streamed or sold or whatever - they've already got their share, and if piracy reduces the number of people outside Japan that watch the anime on Crunchyroll or whatever, oh well! It's not their problem at that point.