The main reason however, is something I've touched on a few times before in this chat thread and the previous one though: It's mostly down to the "anime crash" that occurred between roughly 2006-2009 and the build up to it from 2000-2006.
For a partial explanation that I gave on the subject:
http://www.mmo-champion.com/threads/...1#post35608066
For someone else's insights on the subject:
http://io9.gizmodo.com/what-killed-t...try-1501880696
http://www.rightstufanime.com/anime-...story-of-anime
For raw figures and information on the sales over the past decade or so:
http://aja.gr.jp/english/japan-anime-data
(Just download the 2016 industry report as it has comparison data for the past 15 years or so)
A list of how many anime shows were pumped out each year:
1990 50
1991 39
1992 62
1993 30
1994 38
1995 40
1996 46
1997 50
1998 82
1999 89
2000 64
2001 95
2002 95
2003 111
2004 128
2005 127
2006 181
2007 159
2008 147
2009 146
2010 130
2011 138
2012 155
2013 187
2014 210
When going through the statistical data and anecdotes, it becomes clear that essentially, the anime industry was booming towards the end of the 90's and most of the Japanese companies producing anime decided to cash in hard on the constant uptrend. They did this at the cost of quality and respect for their own audiences.
As you can see from the above figures (just the years + number of anime made per year), in 2006 more anime was pumped out in that year than ever would be until 7 years later. The anime that were pumped out were mostly absolute trash. And I don't mean the usual 'churr durr, this animu is trash' type trash, I mean genuinely terrible stuff, that wouldn't be watched or enjoyed by even the most hardcore fans. Between 2001 and 2006, the generalisation of 'moe' and 'harem' anime was pretty much solidified. Harem and moe anime, with same-face girls copy pasted with different colour hair became a joke even in the West, satirised even on TV shows where the normal audience would have little to no exposure to anime. It's a fact that some of the worst anime ever made came out during this period in particular.
Now that's not to say that there weren't any good shows, there were, however, they were few and far between compared to the sheer quantities of crap they were surrounded by. (To finally get around to your original violence topic) Guts and gore no longer sold any where near as well as easy going harem anime and generic shounen works. So anime studios were just spewing out knock-offs of superior works, cheap and badly made visual novel adaptations and other crap that pandered to the most base of interests among otaku. The need for well drawn, high quality art went out of the window, when things like Kanon, Negima and Lovely Idol could be pumped out fairly effortlessly.
The majority of the truly violent anime that came to represent anime as a more adult media came out in the late 80's and continued to be made until the late 90's. The amount of anime with notable levels of violence or more adult content in general drop off severely during the early-mid 2000s. Outside of fairly fringe, or experimental anime, you rarely see them during this point in time. The whole industry was more focused on hitting larger target audiences, with easier anime to mass produce and make a quick buck on.
By the end of 2006, despite a number of great anime coming out that year, a whole array of anime distributors and consequently studios crashed and ceased to exist, or compressed their businesses and tried to recoup from the sheer fact that, despite almost 50 more anime shows than usual being made that year, sales barely changed in Japan and dropped in the West. This is when people realised the anime bubble had burst and the Japanese owners of the various anime properties started to sweat.
It's in 2008 and onwards, more so in 2010, that we start to see the overall quality of anime increase greatly, as more care and thought is put into actual shows and making sure they'll appeal to a large, but far more specific audience. Harem shows are now a constant, but they're on the back burner, normally being side projects or having minimal budgets. There are exceptions to this rule, normally regarding visual novels and manga that have sold very well. Light novels also become far more of a corner stone in the creation of anime and we see at least a decade of light novel led sales and series. Violent anime is still dotted around here and there, but it's generally very few and far between, with a desire for strong 'teen' equivalent certifications far more appealing than 'adult' ratings.
Anyway. The violence that you see in those mid 2000s anime is fairly tame compared to what was present in the 80's and 90's anime that were popularised. During this period, anime that is now strictly considered 'hentai' was far more mainstream. In the West, anime was viewed at that point in time as being very muchly an adult form of entertainment. Tits and ass were standard faire, even in teen rated anime, drawn in far more gritty styles than the current computer shaded average. Tentacle rape was a media buzzword and hyper violence was associated by proxy with anime. If anything, the 00's were fairly lightweight compared to the 80's and 90's for such content.
It all comes down to the simple matter that people wanted to make more money with anime and so it transformed over time into its young teen friendly style that is currently present today.