True Russia had a whole lot of economic, social and political problems coming from a almost medieval agricultural state to a 1900s industrial state in a few decades. Few if any in the Russian government understood what was going on. The defeat at Port Arthur and the other defeats of the Russo-Japanese war were the straws that broke the camels back so to speak. Adding to the problems the government was archaic, corrupt and bureaucratic. Nicholas II being a micromanager didn't help matters. The truth is it would have taken a military and political genius to have gotten Russia through this trouble which Nicholas II was not. One should also point out he was not a total idiot either.
Also government was autocratic enough to antagonize many people but not nasty enough to put the fear of god in to them so to speak and by 1900 many people have had enough.
Beside the Russo-Japanese war the Crimean war was also a disaster for Russia and the Romanovs. Add to this the defeats of WW I convinced many people the monarchy was unfit to rule Russia.
To Have recovered form the Russo-Japanese War and 1905 revolution 1905-08 Russia needed at least 15-20 years Nicholas II and others realized this. They just did not get the time to recover when in 1914 WW I began. Sadly just as Russia started a major Army expansion and reorganization plan that would have on paper at least made Russia a military super power in 1917. The Germans and Austrians realized this and hence used the Assassination of the Archduke Franz Ferdinand as an excuse to start WW I.