I'm sorry but that whole article is just FUD...
> Input function
Yes, in Python 2, input() is a shortcut for eval(raw_input(...)), and documented as such. Obviously that is not a safe way to parse user input, and therefore it has been changed in Python 3. So this has been fixed, but if you don't read the documentation you probably will keep introducing security issues with whatever programming language.
> Assert statement
If you want to effectively protect against a certain condition, raise an exception! Asserts, on the other hand, exist to help debugging (and documenting) conditions that should never occur by proper API usage. Stripping debugging code when optimizing is common practice, not only with Python.
> Reusable integers
First of all, this behavior isn't part of the Python programming language, but an implementation detail, and a feature as it reduces memory footprint. But even when small integers wouldn't be cached, you would still have the same situation when using the is operator on variables holding the same int object. On the other hand, caching all integers could easily cause a notable memory leak, in particular considering that ints in Python 3 (like longs in Python 2) can be as large as memory available. But either way, there is no good reason to check for identify if you want to compare values, anyway.
> Floats comparison
floats in Python use essentially the native "double" type. Hence they have whatever precision, your CPU has for double precision floating point numbers, actually it is specified in IEEE 754. That way floating point numbers are reasonable fast, while as precise as in most other programming languages. However, if that still isn't enough for your use case, Python also comes with the decimal module (for fixed-point decimal numbers) and the fractions module (for infinite precision fractions).
And as for infinity, while one would expect float('infinity') to be larger than any numerical value, the result of comparing a numerical value with a non-numerical type is undefined. However, Python 3 is more strict and raises a TypeError.
> Private attributes
Class-private attributes (those starting with __) exist to avoid conflicts with class-private attributes of other classes in the class hierarchy, or similar accidents. From my experience that is a feature that is rarely needed, even more rarely in combination with getattr()/setattr()/delattr(). But if you need to dynamically lookup class-private attributes you can still do so like hastattr('_classname__attrname'). After all, self.__attrname is just syntactical sugar for self._classname__attrname.
Also note that private attributes aren't meant as a security mechanism, but merely to avoid accidents. That's not specific to Python; in most object-oriented languages it is possible to to access private attributes, one way or another. However, Python tries to be transparent about that fact, by keeping it simple.
> Module injection
Yes, Python looks in a few places for modules to be imported. That mechanism is quite useful for a couple of reasons, but most notably it's necessary to use modules without installing them system-wide. It can only become a security hole if a malicious user has write access to any location in sys.path, but not to the script, importing the modules, itself. I can hardly think about a scenario like that, and even then I'd rather blame the misconfiguration of the server.
> Code execution on import
Yes, just like every other script language, Python modules can execute arbitrary code on import. That is quite expected, necessary, and not limited to Python. Even if module injection is an issue, it doesn't make anything worse, as you you don't necessarily have to run malicious code on module import but could do it with whatever API is being called. But as outlined above, this is a rather theoretical scenario.
> Shell injection via subprocess
Yes, executing untrusted input, is insecure. That is why the functions in Python's subprocess module, by default, expect a sequence of arguments, rather than a string that is parsed by the system's shell. The documentation clearly explains the consequences of using shell=True. So introducing a shell injection vulnerability by accident, in Python, seems less likely than with most other programming languages.
> Temporary files
If anything, Python is as unsecure as the underlying system, and therefore as most other programming languages too. But CWE-377, the issue the author is talking about, isn't particular easy to exploit in a meaningful way, plus it requires the attacker to already have access to the local temporary directory. Moreover, Python's tempfile module encourages the use of high-level APIs that aren't effected.
> Templating engines
The reason jinja2 doesn't escape HTML markup by default is that it is not an HTML template engine, but a general purpose template engine, which is meant to generate any text-based format. Of course, it is highly recommended to turn on autoescaping when generating HTML/XML output. But enforcing autoescaping would break other formats.