Two somewhat overlapping theories: first, in states where the governments had the most control over the church, atheism was most successful. Many of the churches that were most successful under communism were Catholic Churches (Lithuania, Slovakia, Poland) which obviously had loyalty to Rome, had appointments by Rome, and transnational standards that could not be changed by communist functionaries. Some Orthodox and particularly Protestant churches had heirarchies that were easier to coopt and control. Cardinal Wojtyla could be a focus of anti regime resistance in a way that no Orthodox or Protestant leader could be, his priests could be very involved with Solidarity (which helped the Church's standing in the public eye once the regime fell, too). Notice that Estonia and East Germany were the two most Protestant. Latvia is a big mix of religions so, arguably there's no single hierarchy to coopt (Steve Bruce goes into a little more detail about Latvia in an article comparing the Baltic countries, but I haven't read it in a while). There's an interesting book about ethnic Hungarian Protestants in Romania which seems to imply that minority religious groups, even Protestant ones, could keep their religious traditions better because the government just focused on them less (though they were persecuted in other ways).

Two, in places where national identity was very tied with religious identity, religion remained strong. The most obvious example of this is Poland, but the most illustrative case here is the Czech Republic and Slovakia. I discuss that in an old answer. In Putin's Russia, to be Russian again means to be increasingly tied to the Orthodox Church but this is a fairly new trend (it was less prominent even in Yeltsin's day). I haven't actually looked at the survey data, but I wouldn't be surprised Russia saw a big growth during the past twenty years (unlike Slovakia and Poland, which were religious even right after Communism).

For a bigger post on these sort of dynamics more broadly, see here.

/u/yodatracist makes good points about religious hierarchy differences this map also shows the problem of trying to show to much on one map and bad map design. This map shows which religious group has the plurality in an area, which can cause some problems in analysis.

Looking at the United States as an example you will notice how for the most part it is blue with some red and a bit of brown in the Utah area where their are Mormons. But when you look at the US Census data for religion you start to see problems with this map, Mormons are ~2% of the population, Catholics are 20%-25% of the population, Protestants are ~50% of the population and, non-affiliated are ~16% (numbers vary based on data set and how Protestants are grouped). So you can see how maps such as this can be misleading like for the US having a group that is ~2% of the population being the plurality over a large area and one that is 20%-25% being almost missing from the map.

I am unfamiliar with Estonia and the Czech Republic so I will not comment on them, but Germany is an interesting case due to the religious split between Catholics and Protestants before communism. I can not find good data on the historical religious split in Germany, but I believe it was about 30%-40% Catholic and 60%-70% Protestant. The Catholics were mostly but not exclusively in Bavaria and Western Germany not areas that were communist so their demographics stayed fairly constant. From the modern German census the religious split is 31% Catholic, 31% Protestant, 32% not affiliated, and 5% Islam. The interesting thing though is that while most of the former East Germany is heavily non religious there are parts that are more religious that not. On your map they show up as gray even though there are more believers due to the religious split.

While maps are good for representing data they need some background explanation if there are a lot a variables being shown like in this map because when you look at the data used to create the map it might show something not shown on the map.

Before WW2 parts of Eastern Germany were high industrialized regions. The influence of the workers movement was high and accordingly the relationship to the churches had the tendency of agnosticism, because the churches were on always on the government side since the reformation. The Lutheran Church of eastern Germany tried to keep a moratorium with the state, while the state tried to push to the church into a ideological corner of they are living in the past. This worked very well. In addition the politics of a relative freedom of choosing your own morality supported a life without religion. Because of the shortage of workers women became an important role, the state supported active equality of woman and men incl. free kindergarten. It was easy to get divorced and without the punishment of a financial ruin. So GDR citizens married early (under 20) and most of them were divorced again after some years. Sexuality was much more liberal than in the west which doesn't fit into the morality of a Lutheran church. The amount of Catholics was very small. This sounds positive, but you have to be aware this was only valid until someone interfered with official politics. So most GDR citizens had a very private live without publicity to enjoy their small part of freedom.