If all your columns are numeric, you can use boolean indexing:
In [1]: import pandas as pd
In [2]: df = pd.DataFrame({'a': [0, -1, 2], 'b': [-3, 2, 1]})
In [3]: df
Out[3]:
a b
0 0 -3
1 -1 2
2 2 1
In [4]: df[df < 0] = 0
In [5]: df
Out[5]:
a b
0 0 0
1 0 2
2 2 1
For the more general case, this shows the private method _get_numeric_data:
In [1]: import pandas as pd
In [2]: df = pd.DataFrame({'a': [0, -1, 2], 'b': [-3, 2, 1],
'c': ['foo', 'goo', 'bar']})
In [3]: df
Out[3]:
a b c
0 0 -3 foo
1 -1 2 goo
2 2 1 bar
In [4]: num = df._get_numeric_data()
In [5]: num[num < 0] = 0
In [6]: df
Out[6]:
a b c
0 0 0 foo
1 0 2 goo
2 2 1 bar