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