The flying of flags in England is regulated by the Town & Country Planning Act 1990.
The Act says that you can fly a single national flag from your property from a vertical or horizontal pole without planning permission. However, the flag must not be defaced in any way - it cannot have words or images on it otherwise it is, by law, an advertisment.
The Act does not specify what constitutes a national flag and does not restrict national flags to those of the UK. How the Act applies to national flags of countries not recognised by the UK - Tibet for instance - is, as far as I know, untested.
The flag of the EU is an advertisment under the terms of the Town & Country Planning Act and planning permission must be obtained before flying it. The UK government plans to classify the EU flag as a "supra-national" flag which is exempt from planning controls.
Enforcement of the regulations concerning the flying of flags is the responsibility of the planning department of your local authority. A planning officer can instruct you to remove a flag that does not comply with the regulations and for which you do not have planning permission. If you fail to comply you will be served with a notice instructing you to remove the flag. If you fail to comply with this notice you will be taken to court and the council will remove the flag for you and then bill you for the privelege.
Occasionally, planning officers will instruct members of the public to remove national flags that are not defaced. As long as the flag is not defaced, is on a vertical or horizontal pole, is not accompanied by any other national flags and the flag pole is not a significant structure, the planning officer cannot force you to remove your flag.
In addition to the provisions contained in the Town & Country Planning Act, the right to fly your national flag is deemed to be a human right under international law.