The meaning of this phrase is that there is not enough real democracy in the European Union because its people do not really care about EU elections and because there is not a great deal of respect for its governmental institutions.
The EU has a weak government because it is not really a sovereign state. Each of the EU countries continues to have a fairly strong national identity and people do not necessarily identify much with the EU government. Because of this, they do not care about the government a lot and do not really see it as their own government.
Because the people do not have much faith in the government and do not have that much influence over it, the EU is said to have a democratic deficit.